Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 126 of 279
Found at i:40042350 original size:81 final size:82
Alignment explanation
Indices: 40042181--40042430 Score: 315
Period size: 81 Copynumber: 3.0 Consensus size: 82
40042171 GTTATATGAC
* * *
40042181 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGTTCTAGTTTATAGCGGCGTTTTATCAAAAGC
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTAGTTTTTAGCGGCGTTTTACCAAAAGC
40042246 GCCGCTAATGCTCTAGT
66 GCCGCTAATGCTCTAGT
* * * *
40042263 TTTTAGCGGCGTTTTTTCAAAAGCGCAGCTAATGCTCTGGTTTTTAGTGG-GTTTTACCAAAAGC
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTAGTTTTTAGCGGCGTTTTACCAAAAGC
* *
40042327 GCCGCTAATGGTCTGGT
66 GCCGCTAATGCTCTAGT
* * * * *
40042344 TTTTAGCGGTGTTTTACCAAAAGCGCCGCTATTGCTCTATTTTTTAGCGGCGTTTTTTA-CTAAA
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTAGTTTTTAGCGGCG--TTTTACCAAAA
* *
40042408 GCACCGCTATTGCTCTATGT
64 GCGCCGCTAATGCTCTA-GT
40042428 TTT
1 TTT
40042431 ACAATTTTTG
Statistics
Matches: 142, Mismatches: 22, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
81 70 0.49
82 45 0.32
83 17 0.12
84 10 0.07
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (82 bp):
TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTAGTTTTTAGCGGCGTTTTACCAAAAGC
GCCGCTAATGCTCTAGT
Found at i:40042370 original size:122 final size:123
Alignment explanation
Indices: 40042181--40042401 Score: 354
Period size: 122 Copynumber: 1.8 Consensus size: 123
40042171 GTTATATGAC
* * *
40042181 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGTTCTAGTTTATAGCGGCGTTTTATCAAAAGC
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGGTCTAGTTTATAGCGGCGTTTTACCAAAAGC
40042246 GCCGCTAATGCTCTAGTTTTTAGCGGCGTTTTTTCAAAAGCGCAGCTAATGCTCTGGT
66 GCCGCTAATGCTCTAGTTTTTAGCGGCGTTTTTTCAAAAGCGCAGCTAATGCTCTGGT
* * * *
40042304 TTTTAGTGG-GTTTTACCAAAAGCGCCGCTAATGGTCTGGTTTTTAGCGGTGTTTTACCAAAAGC
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGGTCTAGTTTATAGCGGCGTTTTACCAAAAGC
* *
40042368 GCCGCTATTGCTCTATTTTTTAGCGGCGTTTTTT
66 GCCGCTAATGCTCTAGTTTTTAGCGGCGTTTTTT
40042402 ACTAAAGCAC
Statistics
Matches: 89, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
122 81 0.91
123 8 0.09
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (123 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGGTCTAGTTTATAGCGGCGTTTTACCAAAAGC
GCCGCTAATGCTCTAGTTTTTAGCGGCGTTTTTTCAAAAGCGCAGCTAATGCTCTGGT
Found at i:40049233 original size:45 final size:45
Alignment explanation
Indices: 40049182--40049276 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
40049172 GTAGCAGTAG
*
40049182 CAGTAACAGTAACAATATTCAACACACAAAGTG-CTGAATCTGTAA
1 CAGTAACAGTAACAATATTCAACACACAAAGTGTC-GAATCGGTAA
* * * *
40049227 TAGTAACAGTAACAGTATTCGACACAGAAAGTGTCGAATCGGTAA
1 CAGTAACAGTAACAATATTCAACACACAAAGTGTCGAATCGGTAA
40049272 CAGTA
1 CAGTA
40049277 CGGGTAATAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 42 0.98
46 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (45 bp):
CAGTAACAGTAACAATATTCAACACACAAAGTGTCGAATCGGTAA
Found at i:40049525 original size:40 final size:40
Alignment explanation
Indices: 40049481--40049561 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
40049471 CTTCATTAGA
* * *
40049481 AATTTTACAGTTCAATGCAGTATACATAACATTATTCAGT
1 AATTTCACAGTTCAATGCAGTATACAAAACAATATTCAGT
* * *
40049521 AATTTCACGGTTCAATTCAGTATTCAAAACAATATTCAGT
1 AATTTCACAGTTCAATGCAGTATACAAAACAATATTCAGT
40049561 A
1 A
40049562 TCCCATAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (40 bp):
AATTTCACAGTTCAATGCAGTATACAAAACAATATTCAGT
Found at i:40050453 original size:5 final size:5
Alignment explanation
Indices: 40050443--40050544 Score: 138
Period size: 5 Copynumber: 20.6 Consensus size: 5
40050433 AATAATTAAG
* * *
40050443 TATAT TATAT TATAT TATAT TATA- T-TCT TATAT TCCTA- TATTCT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT T-ATAT TA-TAT TATAT
40050492 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
40050542 TAT
1 TAT
40050545 TATATATAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
3 1 0.01
4 2 0.02
5 79 0.92
6 4 0.05
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:40050475 original size:8 final size:8
Alignment explanation
Indices: 40050462--40050492 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
40050452 TTATATTATA
40050462 TTATATTC
1 TTATATTC
40050470 TTATATTC
1 TTATATTC
*
40050478 CTATATTC
1 TTATATTC
40050486 TTATATT
1 TTATATT
40050493 ATATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (8 bp):
TTATATTC
Found at i:40051687 original size:6 final size:6
Alignment explanation
Indices: 40051668--40051698 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
40051658 GTGTGTCGAA
*
40051668 TACTGT TACCGT TACTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT T
40051699 TCGGATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:40052443 original size:202 final size:202
Alignment explanation
Indices: 40052092--40052494 Score: 779
Period size: 202 Copynumber: 2.0 Consensus size: 202
40052082 TGTTTCTGTG
*
40052092 CGCAAGTTGTAGAAGTCAAGTACTGAACTAGCATCCAAAGCCAGACCCAACTTCAGCAAACTTTT
1 CGCAAGTTGTAGAAGTCAAGTACTGAACCAGCATCCAAAGCCAGACCCAACTTCAGCAAACTTTT
40052157 TGGTGATGTATATTTTCTTTTGGTAATGTGGCATGTACATAGGATTTGTATAAAGGTTATTATGT
66 TGGTGATGTATATTTTCTTTTGGTAATGTGGCATGTACATAGGATTTGTATAAAGGTTATTATGT
40052222 TTTGAATATAAATGTTTTAAAATATTAGAATTACAAGTCTAAGAATTATAATGAAAAAAGTTTAT
131 TTTGAATATAAATGTTTTAAAATATTAGAATTACAAGTCTAAGAATTATAATGAAAAAAGTTTAT
40052287 CCATTTC
196 CCATTTC
*
40052294 CGCAGGTTGTAGAAGTCAAGTACTGAACCAGCATCCAAAGCCAGACCCAACTTCAGCAAACTTTT
1 CGCAAGTTGTAGAAGTCAAGTACTGAACCAGCATCCAAAGCCAGACCCAACTTCAGCAAACTTTT
40052359 TGGTGATGTATATTTTCTTTTGGTAATGTGGCATGTACATAGGATTTGTATAAAGGTTATTATGT
66 TGGTGATGTATATTTTCTTTTGGTAATGTGGCATGTACATAGGATTTGTATAAAGGTTATTATGT
*
40052424 TTTGAATATAAATGTTTTAAATTATTAGAATTACAAGTCTAAGAATTATAATGAAAAAAGTTTAT
131 TTTGAATATAAATGTTTTAAAATATTAGAATTACAAGTCTAAGAATTATAATGAAAAAAGTTTAT
40052489 CCATTT
196 CCATTT
40052495 TGTTCAACAT
Statistics
Matches: 198, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
202 198 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (202 bp):
CGCAAGTTGTAGAAGTCAAGTACTGAACCAGCATCCAAAGCCAGACCCAACTTCAGCAAACTTTT
TGGTGATGTATATTTTCTTTTGGTAATGTGGCATGTACATAGGATTTGTATAAAGGTTATTATGT
TTTGAATATAAATGTTTTAAAATATTAGAATTACAAGTCTAAGAATTATAATGAAAAAAGTTTAT
CCATTTC
Found at i:40052749 original size:5 final size:5
Alignment explanation
Indices: 40052739--40052763 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
40052729 TTTCTTTTAT
40052739 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
40052764 TTTTAATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:40057412 original size:5 final size:5
Alignment explanation
Indices: 40057394--40057437 Score: 65
Period size: 5 Copynumber: 9.0 Consensus size: 5
40057384 TTTCTTTTAT
40057394 ATATA ATAATA ATATA ATATA ATATA ATAT- A-ATA ATATA ATATA
1 ATATA AT-ATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
40057438 CTTAATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 2 0.06
4 2 0.06
5 27 0.75
6 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:40057412 original size:8 final size:8
Alignment explanation
Indices: 40057399--40057435 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
40057389 TTTATATATA
40057399 ATAATAAT
1 ATAATAAT
40057407 ATAAT-AT
1 ATAATAAT
40057414 A-ATATAAT
1 ATA-ATAAT
40057422 ATAATAAT
1 ATAATAAT
40057430 ATAATA
1 ATAATA
40057436 TACTTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
6 1 0.04
7 5 0.19
8 19 0.73
9 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAATAAT
Found at i:40057415 original size:13 final size:14
Alignment explanation
Indices: 40057391--40057437 Score: 69
Period size: 13 Copynumber: 3.3 Consensus size: 14
40057381 TTGTTTCTTT
40057391 TATATATAATAATAA
1 TATATATAAT-ATAA
40057406 TATAATATAATATAA
1 TAT-ATATAATATAA
40057421 TATA-ATAATATAA
1 TATATATAATATAA
40057434 TATA
1 TATA
40057438 CTTAATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.42
14 1 0.03
15 10 0.32
16 7 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TATATATAATATAA
Found at i:40059078 original size:52 final size:52
Alignment explanation
Indices: 40059007--40059210 Score: 390
Period size: 52 Copynumber: 3.9 Consensus size: 52
40058997 ATCAAGTGAC
40059007 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
40059059 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
40059111 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
* *
40059163 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
40059211 AGTGATAAGT
Statistics
Matches: 150, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 150 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (52 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:40059231 original size:37 final size:37
Alignment explanation
Indices: 40059184--40059293 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
40059174 TGATAGCTTC
*
40059184 GGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
* *
40059221 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
40059258 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
40059293 G
1 G
40059294 ATCATACGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.25
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
Found at i:40060177 original size:43 final size:43
Alignment explanation
Indices: 40060116--40060254 Score: 136
Period size: 43 Copynumber: 3.2 Consensus size: 43
40060106 AAACAAAAGT
* * *
40060116 TATTGGCACACATAGTGCATTATCGGGCAAGCCAAAGCAATTA
1 TATTGACACACATAGTGCATTATCGGACAAACCAAAGCAATTA
* * *
40060159 TATTGACACACA-AGGTGCATTGTTGGACAAACCAGAGCAATTA
1 TATTGACACACATA-GTGCATTATCGGACAAACCAAAGCAATTA
* * * * * * * *
40060202 TATTGACACGCATAGTGCATCATTGAATAAATCGAAGTAATTA
1 TATTGACACACATAGTGCATTATCGGACAAACCAAAGCAATTA
40060245 TATTGACACA
1 TATTGACACA
40060255 TAAGGAATAT
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
42 1 0.01
43 76 0.97
44 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (43 bp):
TATTGACACACATAGTGCATTATCGGACAAACCAAAGCAATTA
Found at i:40060271 original size:86 final size:86
Alignment explanation
Indices: 40060150--40060329 Score: 211
Period size: 86 Copynumber: 2.1 Consensus size: 86
40060140 GGGCAAGCCA
** ** *
40060150 AAGCAATTATATTGACACACAAGGTGCATTGTTGGACAAACCAG-AGCAATTATATT-GACACGC
1 AAGCAATTATATTGACACACAAGGAACATCATTGGACAAA-CAGAAACAATTATATTAG-CACGC
*
40060213 ATAGTGCATCATTGAATAAATCG
64 ATAGTGCATCATTGAATAAACCG
* * * ** *
40060236 AAGTAATTATATTGACACATAAGGAATATCATTGGACAAATTGAAACAATTATATTAGTACGCAT
1 AAGCAATTATATTGACACACAAGGAACATCATTGGACAAACAGAAACAATTATATTAGCACGCAT
*
40060301 AGTGCATCATTGGATAAACCG
66 AGTGCATCATTGAATAAACCG
40060322 AAGCAATT
1 AAGCAATT
40060330 GGTTGCTTTG
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
85 1 0.01
86 76 0.97
87 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (86 bp):
AAGCAATTATATTGACACACAAGGAACATCATTGGACAAACAGAAACAATTATATTAGCACGCAT
AGTGCATCATTGAATAAACCG
Found at i:40060329 original size:43 final size:41
Alignment explanation
Indices: 40060126--40060329 Score: 133
Period size: 43 Copynumber: 4.8 Consensus size: 41
40060116 TATTGGCACA
* * * * * *
40060126 CATAGTGCATTATCGGGCAAGCCAAAGCAATTATATTGACA
1 CATAGTGCATCATTGGACAAACCGAAGCAATTATATTGACG
* **
40060167 CACAAGGTGCATTGTTGGACAAACC-AGAGCAATTATATTGACACG
1 CA-TA-GTGCATCATTGGACAAACCGA-AGCAATTATATTG--ACG
* * * * *
40060212 CATAGTGCATCATTGAATAAATCGAAGTAATTATATTGACA
1 CATAGTGCATCATTGGACAAACCGAAGCAATTATATTGACG
* ** *
40060253 CATAAG-GAATATCATTGGACAAATTGAAACAATTATATTAGTACG
1 CAT-AGTG--CATCATTGGACAAACCGAAGCAATTATATT-G-ACG
*
40060298 CATAGTGCATCATTGGATAAACCGAAGCAATT
1 CATAGTGCATCATTGGACAAACCGAAGCAATT
40060330 GGTTGCTTTG
Statistics
Matches: 125, Mismatches: 26, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
41 8 0.06
42 4 0.03
43 98 0.78
44 5 0.04
45 10 0.08
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26
Consensus pattern (41 bp):
CATAGTGCATCATTGGACAAACCGAAGCAATTATATTGACG
Found at i:40072730 original size:6 final size:6
Alignment explanation
Indices: 40072719--40072759 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
40072709 TGGCTTATAC
*
40072719 CCCTTG CCCTTG TCCTTG CCCTTG CCCTTG CCCTTG CCCTT
1 CCCTTG CCCTTG CCCTTG CCCTTG CCCTTG CCCTTG CCCTT
40072760 CACTTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.15, T:0.37
Consensus pattern (6 bp):
CCCTTG
Found at i:40073777 original size:60 final size:61
Alignment explanation
Indices: 40073666--40073808 Score: 153
Period size: 60 Copynumber: 2.4 Consensus size: 61
40073656 TAACTTGAAT
* * * * * * *
40073666 AAAAATAGTTTAAGTCCTAATGTGGGAACATTTGTCAAGTTTAGGCCCTAACTTA-CCAAA
1 AAAAAAAGTTTAAGTCCTAATGTGAGAACAATTGCCAAATTCAGGCCCTAACTTAGACAAA
* * **
40073726 AAAAAAAGTTCAAGTCCTAATGTGAGAATAATTGCCAAATTCAGGGTCTAACTTAGACAAA
1 AAAAAAAGTTTAAGTCCTAATGTGAGAACAATTGCCAAATTCAGGCCCTAACTTAGACAAA
* * *
40073787 AAAATAATTTTAAATCCTAATG
1 AAAAAAAGTTTAAGTCCTAATG
40073809 AAAGAAAAAT
Statistics
Matches: 67, Mismatches: 15, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
60 45 0.67
61 22 0.33
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (61 bp):
AAAAAAAGTTTAAGTCCTAATGTGAGAACAATTGCCAAATTCAGGCCCTAACTTAGACAAA
Found at i:40092314 original size:15 final size:16
Alignment explanation
Indices: 40092294--40092363 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 16
40092284 ACTATAAAAC
40092294 ATTTATTA-TGAATAT
1 ATTTATTATTGAATAT
*
40092309 ATTTATAATTGTAATAAAT
1 ATTTATTATTG-AAT--AT
*
40092328 ATTTATTATT-AAAAT
1 ATTTATTATTGAATAT
*
40092343 A-TTAATATTGAATATT
1 ATTTATTATTGAATA-T
40092359 ATTTA
1 ATTTA
40092364 AAATTTATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
14 7 0.16
15 13 0.30
16 4 0.09
17 8 0.19
19 11 0.26
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (16 bp):
ATTTATTATTGAATAT
Found at i:40092882 original size:39 final size:39
Alignment explanation
Indices: 40092828--40092907 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
40092818 AATACTTAAA
40092828 AAATTAAATTGTAGTTTTTAGTTTTTCATGTATATATAT
1 AAATTAAATTGTAGTTTTTAGTTTTTCATGTATATATAT
40092867 AAATTAAATTGTAGTTTTTAGTTTTTCATGTATATATAT
1 AAATTAAATTGTAGTTTTTAGTTTTTCATGTATATATAT
40092906 AA
1 AA
40092908 GAATGATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.53
Consensus pattern (39 bp):
AAATTAAATTGTAGTTTTTAGTTTTTCATGTATATATAT
Found at i:40111731 original size:24 final size:22
Alignment explanation
Indices: 40111688--40111732 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
40111678 AACCTTTTAA
*
40111688 TTATTAATTAAAAAATGTTATT
1 TTATTAATTAAAAAACGTTATT
*
40111710 TTATTGAACTTAAAAGACGTTAT
1 TTATT-AA-TTAAAAAACGTTAT
40111733 AGTAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 2 0.11
24 12 0.63
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.44
Consensus pattern (22 bp):
TTATTAATTAAAAAACGTTATT
Found at i:40113202 original size:22 final size:22
Alignment explanation
Indices: 40113158--40113202 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
40113148 TTGACTTTAA
**
40113158 TTTTTTAAATTTGATATTTAAT
1 TTTTTTAAATTTGATATCAAAT
* *
40113180 TTTTTTTAATTTGGTATCAAAT
1 TTTTTTAAATTTGATATCAAAT
40113202 T
1 T
40113203 GGACAACAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (22 bp):
TTTTTTAAATTTGATATCAAAT
Found at i:40113972 original size:29 final size:29
Alignment explanation
Indices: 40113931--40114008 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 29
40113921 TTTTAATAAG
* *
40113931 TAAATTTGA-CACTAAATTTTTATGTTAT
1 TAAATTTTACCACTAAATTTTAATGTTAT
* *
40113959 TAAATTTTACCACTAAACTTTAAATTTTAT
1 TAAATTTTACCACTAAA-TTTTAATGTTAT
* *
40113989 TAATTTTTGCCAC-AAATTTT
1 TAAATTTTACCACTAAATTTT
40114009 CATTTTTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
28 11 0.27
29 10 0.24
30 20 0.49
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.49
Consensus pattern (29 bp):
TAAATTTTACCACTAAATTTTAATGTTAT
Found at i:40123774 original size:12 final size:12
Alignment explanation
Indices: 40123757--40123789 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
40123747 TAAGATGGTG
40123757 AAATAAATAAAA
1 AAATAAATAAAA
40123769 AAATAAA-AAAA
1 AAATAAATAAAA
40123780 AAATACAATA
1 AAATA-AATA
40123790 GGTCTCCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.47
12 9 0.47
13 1 0.05
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATAAATAAAA
Found at i:40131237 original size:15 final size:15
Alignment explanation
Indices: 40131217--40131268 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
40131207 ACTATAAAAA
40131217 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
40131232 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
40131251 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
40131266 ATT
1 ATT
40131269 ACTATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:40131396 original size:22 final size:21
Alignment explanation
Indices: 40131349--40131403 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
40131339 AATAAAGTTA
*
40131349 AAATATTAAA-TA-ATTTATT
1 AAATAATAAATTATATTTATT
40131368 AAATAATAAATTATATTTATT
1 AAATAATAAATTATATTTATT
* *
40131389 ATATTAATAATTTAT
1 A-AATAATAAATTAT
40131404 TATATGAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.30
20 2 0.07
21 8 0.27
22 11 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATAATAAATTATATTTATT
Found at i:40131403 original size:16 final size:16
Alignment explanation
Indices: 40131382--40131414 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
40131372 AATAAATTAT
*
40131382 ATTTATTATATTAATA
1 ATTTATTATATGAATA
40131398 ATTTATTATATGAATA
1 ATTTATTATATGAATA
40131414 A
1 A
40131415 ATATAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
ATTTATTATATGAATA
Found at i:40134351 original size:11 final size:11
Alignment explanation
Indices: 40134332--40134379 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
40134322 TAGCTATTTA
40134332 TAATAAAATAT
1 TAATAAAATAT
*
40134343 TAGTAAAATAT
1 TAATAAAATAT
* *
40134354 CTCATTAAAATAA
1 -T-AATAAAATAT
40134367 TAATAAAATAT
1 TAATAAAATAT
40134378 TA
1 TA
40134380 TTTATCAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
11 20 0.67
12 2 0.07
13 8 0.27
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:40137645 original size:14 final size:14
Alignment explanation
Indices: 40137607--40137639 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40137597 GCTTTTTCTT
40137607 AAAA-AAAAAAAGA
1 AAAAGAAAAAAAGA
40137620 AAAAGAAAAAAAGA
1 AAAAGAAAAAAAGA
*
40137634 AGAAGA
1 AAAAGA
40137640 TTAAAACGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAGA
Found at i:40141194 original size:19 final size:18
Alignment explanation
Indices: 40141170--40141207 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
40141160 TCTTATATTC
*
40141170 ATATTTTAAATTAGTTTTT
1 ATATTTAAAATTA-TTTTT
40141189 ATATTTAAAATTATTTTT
1 ATATTTAAAATTATTTTT
40141207 A
1 A
40141208 ATTGAGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
ATATTTAAAATTATTTTT
Found at i:40146945 original size:33 final size:33
Alignment explanation
Indices: 40146908--40146976 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
40146898 ATAGACATGG
*
40146908 TTTTTCTTGAAAATTTAAGAAATTAAAGGCTAT
1 TTTTTCTTGAAAAATTAAGAAATTAAAGGCTAT
*
40146941 TTTTTCTTGAAAAATTAAGAAATTAAGGGCTAT
1 TTTTTCTTGAAAAATTAAGAAATTAAAGGCTAT
40146974 TTT
1 TTT
40146977 AGACTGGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (33 bp):
TTTTTCTTGAAAAATTAAGAAATTAAAGGCTAT
Found at i:40152250 original size:47 final size:46
Alignment explanation
Indices: 40152134--40152260 Score: 173
Period size: 46 Copynumber: 2.7 Consensus size: 46
40152124 ATAATCTCAC
* * * * * *
40152134 CCATAATGAACTCGGAACGCAACTTAACAAGCTCGGGTGTTTGCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCAGATGCTTGCAT
*
40152180 CCATAATGAACTCGGAACACAACTCAACGAGTTCAGATGCTTGCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCAGATGCTTGCAT
*
40152226 CCATAGGTGAACTCGGAACGCAACTCAACGAGTTC
1 CCATA-ATGAACTCGGAACGCAACTCAACGAGTTC
40152261 GGATCTCAAT
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
46 44 0.62
47 27 0.38
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGTTCAGATGCTTGCAT
Found at i:40155812 original size:45 final size:46
Alignment explanation
Indices: 40155723--40155810 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 46
40155713 GTATAGTTAT
*
40155723 TTTAAATTTTAATTAAATTCATCTATATTTGAAAATAAATAAAATA
1 TTTAAATTTTAATTAAATTCATATATATTTGAAAATAAATAAAATA
* *
40155769 TTTAAATTTT-TTTAAGTTCATATA-ATTT-AAAATAAATTAAAA
1 TTTAAATTTTAATTAAATTCATATATATTTGAAAATAAA-TAAAA
40155811 ATGTTATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 8 0.21
44 9 0.24
45 11 0.29
46 10 0.26
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (46 bp):
TTTAAATTTTAATTAAATTCATATATATTTGAAAATAAATAAAATA
Found at i:40161175 original size:44 final size:45
Alignment explanation
Indices: 40161106--40161198 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 45
40161096 TATGATTTAA
*
40161106 ATAATATACTTTTTTATAACTTTATAAAATACACAAATTATTT-TT
1 ATAATATAATTTTTTATAACTTTATAAAATA-ACAAATTATTTGTT
* * *
40161151 ATAATATAATTTTTTAGT-AC-TTATAATATAAGAAATTTTTTGTT
1 ATAATATAATTTTTTA-TAACTTTATAAAATAACAAATTATTTGTT
40161195 ATAA
1 ATAA
40161199 CCATCTCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
43 9 0.21
44 15 0.36
45 17 0.40
46 1 0.02
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.49
Consensus pattern (45 bp):
ATAATATAATTTTTTATAACTTTATAAAATAACAAATTATTTGTT
Found at i:40165756 original size:10 final size:10
Alignment explanation
Indices: 40165741--40165775 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
40165731 AAGGAAAACC
40165741 TATATAAATA
1 TATATAAATA
40165751 TATATAAATA
1 TATATAAATA
* *
40165761 AATATATATA
1 TATATAAATA
40165771 TATAT
1 TATAT
40165776 GGATCTTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TATATAAATA
Found at i:40165763 original size:14 final size:14
Alignment explanation
Indices: 40165744--40165770 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40165734 GAAAACCTAT
40165744 ATAAATATATATAA
1 ATAAATATATATAA
40165758 ATAAATATATATA
1 ATAAATATATATA
40165771 TATATGGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATAAATATATATAA
Found at i:40172123 original size:19 final size:19
Alignment explanation
Indices: 40172099--40172137 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
40172089 CTTAAGGTCC
40172099 GTGTTTAATTGAAGTTTGG
1 GTGTTTAATTGAAGTTTGG
40172118 GTGTTTAATTGAAGTTTGG
1 GTGTTTAATTGAAGTTTGG
40172137 G
1 G
40172138 CTAAATATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (19 bp):
GTGTTTAATTGAAGTTTGG
Found at i:40189541 original size:13 final size:13
Alignment explanation
Indices: 40189523--40189550 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40189513 TACCGGTTGT
40189523 CTTAACCATTAAG
1 CTTAACCATTAAG
40189536 CTTAACCATTAAG
1 CTTAACCATTAAG
40189549 CT
1 CT
40189551 CATAATCTTC
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:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (13 bp):
CTTAACCATTAAG
Found at i:40196738 original size:30 final size:29
Alignment explanation
Indices: 40196704--40196765 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
40196694 GTGTTTTACT
40196704 AAAATTAACTAATTTCTGTAT-ATTTTTAAA
1 AAAATTAACTAATTT-T-TATAATTTTTAAA
* *
40196734 AAAATTGACTTATTTTTATAATTTTTAAA
1 AAAATTAACTAATTTTTATAATTTTTAAA
40196763 AAA
1 AAA
40196766 TTAGCTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 3 0.10
29 13 0.45
30 13 0.45
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (29 bp):
AAAATTAACTAATTTTTATAATTTTTAAA
Found at i:40196758 original size:28 final size:27
Alignment explanation
Indices: 40196704--40196784 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
40196694 GTGTTTTACT
* *
40196704 AAAATTAACTAATTTCTGTATATTTTTAAA
1 AAAATT-ACTTATTT-T-TATAATTTTAAA
*
40196734 AAAATTGACTTATTTTTATAATTTTTAA
1 AAAATT-ACTTATTTTTATAATTTTAAA
*
40196762 AAAATTAGCTT-TTTTGATAATTT
1 AAAATTA-CTTATTTTTATAATTT
40196785 ATTCTCATAG
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
27 12 0.27
28 19 0.42
29 1 0.02
30 13 0.29
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (27 bp):
AAAATTACTTATTTTTATAATTTTAAA
Found at i:40196776 original size:27 final size:29
Alignment explanation
Indices: 40196725--40196784 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 29
40196715 ATTTCTGTAT
*
40196725 ATTTTTAAAAAAATTGACTTATTTTTATA
1 ATTTTTAAAAAAATTGACTTATTTTGATA
40196754 ATTTTT-AAAAAATT-AGCTT-TTTTGATA
1 ATTTTTAAAAAAATTGA-CTTATTTTGATA
40196781 ATTT
1 ATTT
40196785 ATTCTCATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 12 0.41
28 11 0.38
29 6 0.21
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (29 bp):
ATTTTTAAAAAAATTGACTTATTTTGATA
Found at i:40197018 original size:16 final size:17
Alignment explanation
Indices: 40196999--40197031 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40196989 ATATTTCATT
40196999 AATAAA-AAAAAGTAAA
1 AATAAATAAAAAGTAAA
*
40197015 AATAAATAAACAGTAAA
1 AATAAATAAAAAGTAAA
40197032 GATTTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (17 bp):
AATAAATAAAAAGTAAA
Found at i:40197063 original size:24 final size:25
Alignment explanation
Indices: 40197036--40197082 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
40197026 AGTAAAGATT
* *
40197036 TATATTATTAATTA-AATAAAAATA
1 TATATTATAAATTATAAAAAAAATA
40197060 TATATTATAAATTATAAAAAAAA
1 TATATTATAAATTATAAAAAAAA
40197083 ATGGTACTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TATATTATAAATTATAAAAAAAATA
Found at i:40197741 original size:26 final size:26
Alignment explanation
Indices: 40197708--40197757 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
40197698 TCATGGTTAC
*
40197708 TAATATATATATATTT-CAATTTAAA
1 TAATATATAAATATTTACAATTTAAA
*
40197733 TAATCATATAAATCTTTACAATTTA
1 TAAT-ATATAAATATTTACAATTTA
40197758 TTTTATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 10 0.48
27 7 0.33
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (26 bp):
TAATATATAAATATTTACAATTTAAA
Found at i:40199310 original size:5 final size:5
Alignment explanation
Indices: 40199300--40199363 Score: 96
Period size: 5 Copynumber: 12.8 Consensus size: 5
40199290 AATTATGTTT
40199300 TTATA TTATA TTATTA TTA-A -TATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
40199349 TTATTA TTATA TTAT
1 TTA-TA TTATA TTAT
40199364 TATATATATG
Statistics
Matches: 55, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 41 0.75
6 10 0.18
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:40199314 original size:8 final size:8
Alignment explanation
Indices: 40199300--40199368 Score: 67
Period size: 8 Copynumber: 8.8 Consensus size: 8
40199290 AATTATGTTT
40199300 TTATATTA
1 TTATATTA
40199308 -TATTATTA
1 TTA-TATTA
40199316 TTA-ATATA
1 TTATAT-TA
40199324 TTATATTA
1 TTATATTA
40199332 -TAT-TATA
1 TTATAT-TA
40199339 TTATATTA
1 TTATATTA
40199347 -TATTATTA
1 TTA-TATTA
40199355 TTATATTA
1 TTATATTA
40199363 TTATAT
1 TTATAT
40199369 ATATGACAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
6 1 0.02
7 11 0.21
8 33 0.63
9 7 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTATATTA
Found at i:40199316 original size:3 final size:3
Alignment explanation
Indices: 40199303--40199366 Score: 63
Period size: 3 Copynumber: 24.0 Consensus size: 3
40199293 TATGTTTTTA
*
40199303 TAT TA- TAT TAT TAT TAA TA- TAT TA- TAT TA- TAT TA- TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40199345 TA- TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
40199367 ATATATGACA
Statistics
Matches: 52, Mismatches: 1, Indels: 16
0.75 0.01 0.23
Matches are distributed among these distances:
2 16 0.31
3 36 0.69
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:40199438 original size:40 final size:40
Alignment explanation
Indices: 40199381--40199476 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
40199371 ATGACAAAGA
40199381 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
1 AAGAAAG-AAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
* *
40199422 GAGAAAGAAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
*
40199462 AAGGAAGGAAAGAAA
1 AA-GAAAGAAAGAAA
40199477 GAAAGAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 33 0.66
41 17 0.34
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (40 bp):
AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
Found at i:40200889 original size:41 final size:39
Alignment explanation
Indices: 40200841--40200952 Score: 111
Period size: 37 Copynumber: 2.9 Consensus size: 39
40200831 TCGACCTTGA
40200841 GTCGATGAGACACTGGGTGTCATACTATTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCA-ACTATTACTTCGGATAG
* ** ** * *
40200881 ATTCGATGAGGTACTGGGTACCAAC--TTACTTCGGCTTG
1 -GTCGATGAGACACTGGGTGTCAACTATTACTTCGGATAG
* *
40200919 GCCGATGAGACACTGGGTGTCAACTATTGCTTCG
1 GTCGATGAGACACTGGGTGTCAACTATTACTTCG
40200953 AACTATCCGA
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
37 18 0.33
38 11 0.20
39 7 0.13
40 2 0.04
41 17 0.31
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (39 bp):
GTCGATGAGACACTGGGTGTCAACTATTACTTCGGATAG
Found at i:40206671 original size:68 final size:67
Alignment explanation
Indices: 40206562--40206693 Score: 246
Period size: 68 Copynumber: 2.0 Consensus size: 67
40206552 CACCGAAGCC
*
40206562 ATAGCCTTGCCATGGTCTTACACGGTTCACATATCATACCGAAGCCATATCCCCGACATGGTCTC
1 ATAGCCTTGCCATGGTCTTACACGGTTCACATATCATACCGAAGCCATATCCCAGACATGGTCTC
40206627 AT
66 AT
40206629 NATAGCCTTGCCATGGTCTTACACGGTTCACATATCATACCGAAGCCATATCCCAGACATGGTCT
1 -ATAGCCTTGCCATGGTCTTACACGGTTCACATATCATACCGAAGCCATATCCCAGACATGGTCT
40206694 TATACGGAAT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (67 bp):
ATAGCCTTGCCATGGTCTTACACGGTTCACATATCATACCGAAGCCATATCCCAGACATGGTCTC
AT
Found at i:40213098 original size:15 final size:16
Alignment explanation
Indices: 40213080--40213109 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40213070 ATATAAATTA
40213080 AAAAATTAAA-AAAAT
1 AAAAATTAAATAAAAT
40213095 AAAAATTAAATAAAA
1 AAAAATTAAATAAAA
40213110 GGTAATCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAAATTAAATAAAAT
Found at i:40223509 original size:13 final size:14
Alignment explanation
Indices: 40223488--40223516 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
40223478 TGAAAAATGG
40223488 ATTAGAAAATATTT
1 ATTAGAAAATATTT
40223502 ATTA-AAAATATTT
1 ATTAGAAAATATTT
40223515 AT
1 AT
40223517 GAAGTTAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
ATTAGAAAATATTT
Found at i:40224079 original size:31 final size:32
Alignment explanation
Indices: 40224030--40224093 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
40224020 ATATTAAATA
*
40224030 AGATATTTATTAATTAAATA-ATTATATTATG
1 AGATATTTATTAATTAAATATATTAAATTATG
*
40224061 AGATTTTTATGTAA-TAAATATATTAAATTATG
1 AGATATTTAT-TAATTAAATATATTAAATTATG
40224093 A
1 A
40224094 CAAATGTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (32 bp):
AGATATTTATTAATTAAATATATTAAATTATG
Found at i:40224409 original size:15 final size:15
Alignment explanation
Indices: 40224386--40224433 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
40224376 TATCAAATTT
40224386 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
40224401 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
40224416 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
40224430 ATAT
1 ATAT
40224434 AATATATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:40224822 original size:23 final size:23
Alignment explanation
Indices: 40224794--40224842 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
40224784 TAATATTCCG
40224794 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
40224817 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
40224840 GGT
1 GGT
40224843 ATCTATCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.08, C:0.04, G:0.41, T:0.47
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGATATTCT
Found at i:40224956 original size:18 final size:19
Alignment explanation
Indices: 40224935--40224975 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
40224925 AATGAAATGA
40224935 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
40224953 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
40224972 GAAA
1 GAAA
40224976 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:40239062 original size:30 final size:30
Alignment explanation
Indices: 40239026--40239089 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
40239016 NNNNNNNNNN
*
40239026 TAGTGGAGTTGGTGGTGGAAAAGGTGTGGC
1 TAGTGGAGTTGGTGGTGGAAAAGGAGTGGC
40239056 TAGTGGAGTTGGTGGTGGAAAAGGAGTGGC
1 TAGTGGAGTTGGTGGTGGAAAAGGAGTGGC
40239086 TAGT
1 TAGT
40239090 TGAGAAAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.22, C:0.03, G:0.48, T:0.27
Consensus pattern (30 bp):
TAGTGGAGTTGGTGGTGGAAAAGGAGTGGC
Found at i:40240206 original size:6 final size:6
Alignment explanation
Indices: 40240197--40240228 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
40240187 TTTTAATTAC
40240197 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA AT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA AT
40240229 ATAATCAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTTA
Found at i:40246121 original size:24 final size:24
Alignment explanation
Indices: 40246094--40246164 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 24
40246084 ATGTTTTACA
40246094 TAGGGTGGTAAATTAATTGTTATG
1 TAGGGTGGTAAATTAATTGTTATG
**
40246118 TAGGGACG--AA-T-ATTGTTA-G
1 TAGGGTGGTAAATTAATTGTTATG
*
40246137 CTGAGGGTGGTAAATTAAGTGTTATG
1 -T-AGGGTGGTAAATTAATTGTTATG
40246163 TA
1 TA
40246165 CTGACGAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 14
0.65 0.09 0.26
Matches are distributed among these distances:
19 1 0.03
20 8 0.23
21 6 0.17
22 2 0.06
23 2 0.06
24 8 0.23
25 7 0.20
26 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.31, T:0.37
Consensus pattern (24 bp):
TAGGGTGGTAAATTAATTGTTATG
Found at i:40246146 original size:45 final size:45
Alignment explanation
Indices: 40246095--40246186 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
40246085 TGTTTTACAT
* *
40246095 AGGGTGGTAAATTAATTGTTATGTAGGGACGAATATTGTTAGCTG
1 AGGGTGGTAAATTAAGTGTTATGTACGGACGAATATTGTTAGCTG
*
40246140 AGGGTGGTAAATTAAGTGTTATGTACTGACGAATATTGTTAGCTG
1 AGGGTGGTAAATTAAGTGTTATGTACGGACGAATATTGTTAGCTG
40246185 AG
1 AG
40246187 TCCGCACCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.29, C:0.05, G:0.30, T:0.35
Consensus pattern (45 bp):
AGGGTGGTAAATTAAGTGTTATGTACGGACGAATATTGTTAGCTG
Found at i:40251501 original size:37 final size:37
Alignment explanation
Indices: 40251451--40251523 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
40251441 AAAAAATTTC
40251451 TGTTTTGTTATGATGTGAATTTTCAATTGGTACTAGT
1 TGTTTTGTTATGATGTGAATTTTCAATTGGTACTAGT
40251488 TGTTTTGTTATGATGTGAATTTTCAATTGGTACTAG
1 TGTTTTGTTATGATGTGAATTTTCAATTGGTACTAG
40251524 CTGTACCAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.22, C:0.05, G:0.22, T:0.51
Consensus pattern (37 bp):
TGTTTTGTTATGATGTGAATTTTCAATTGGTACTAGT
Found at i:40252237 original size:15 final size:16
Alignment explanation
Indices: 40252209--40252238 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40252199 TTTTATTTGC
40252209 AAAGAAGAAGAATAAG
1 AAAGAAGAAGAATAAG
40252225 AAAGAAG-AGAATAA
1 AAAGAAGAAGAATAA
40252239 TTGTATGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (16 bp):
AAAGAAGAAGAATAAG
Found at i:40261193 original size:17 final size:17
Alignment explanation
Indices: 40261171--40261225 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 17
40261161 TAATCAAGAA
40261171 AAATATATAAAATTTTT
1 AAATATATAAAATTTTT
*
40261188 -AA-ATATAAAA-TTTA
1 AAATATATAAAATTTTT
40261202 AAATAATATAAATATTTTTT
1 AAAT-ATATAAA-A-TTTTT
40261222 AAAT
1 AAAT
40261226 TTTAATCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 10 0.33
16 2 0.07
17 7 0.23
18 1 0.03
20 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATATATAAAATTTTT
Found at i:40262030 original size:29 final size:29
Alignment explanation
Indices: 40261997--40262063 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 29
40261987 AAAATTATTA
40261997 AAAAAAGTA-AACTTATTTCTATCTTTACT
1 AAAAAA-TATAACTTATTTCTATCTTTACT
*
40262026 AAAAAATATTACTTATTTCTATCTTTACT
1 AAAAAATATAACTTATTTCTATCTTTACT
40262055 AAAAAATAT
1 AAAAAATAT
40262064 TGTTATTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 2 0.06
29 34 0.94
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (29 bp):
AAAAAATATAACTTATTTCTATCTTTACT
Found at i:40262070 original size:28 final size:29
Alignment explanation
Indices: 40262007--40262064 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
40261997 AAAAAAGTAA
40262007 ACTTATTTCTATCTTTACTAAAAAATATT
1 ACTTATTTCTATCTTTACTAAAAAATATT
40262036 ACTTATTTCTATCTTTACTAAAAAATATT
1 ACTTATTTCTATCTTTACTAAAAAATATT
40262065 GTTATTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (29 bp):
ACTTATTTCTATCTTTACTAAAAAATATT
Found at i:40268801 original size:16 final size:16
Alignment explanation
Indices: 40268780--40268810 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40268770 GATATTTTAA
40268780 TATATTATATTAATAT
1 TATATTATATTAATAT
*
40268796 TATATTATGTTAATA
1 TATATTATATTAATA
40268811 AAATAATAAA
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:0.03, T:0.55
Consensus pattern (16 bp):
TATATTATATTAATAT
Found at i:40270025 original size:27 final size:27
Alignment explanation
Indices: 40269973--40270041 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 27
40269963 ATGCCTTATT
**
40269973 GGTGTGTTTGGGAGGATATATTATACC
1 GGTGTGTTTGGGAGGATATACAATACC
*
40270000 GGTGTGTTAT-GGAGGATTTACAATACTCC
1 GGTGTGTT-TGGGAGGATATACAATA--CC
40270029 TGGTGTGTTTGGG
1 -GGTGTGTTTGGG
40270042 TTGGATATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
27 20 0.59
28 1 0.03
29 3 0.09
30 10 0.29
ACGTcount: A:0.19, C:0.09, G:0.35, T:0.38
Consensus pattern (27 bp):
GGTGTGTTTGGGAGGATATACAATACC
Found at i:40272425 original size:13 final size:14
Alignment explanation
Indices: 40272393--40272426 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
40272383 AGTATTTGGG
*
40272393 GTTCTAGGTTCGAT
1 GTTCAAGGTTCGAT
40272407 GTTCAAGGTTCGA-
1 GTTCAAGGTTCGAT
40272420 GTTCAAG
1 GTTCAAG
40272427 ATTTAAAAGT
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:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (14 bp):
GTTCAAGGTTCGAT
Found at i:40272459 original size:21 final size:21
Alignment explanation
Indices: 40272411--40272459 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
40272401 TTCGATGTTC
40272411 AAGGTTCGAGTTCAAGATTTA
1 AAGGTTCGAGTTCAAGATTTA
* *
40272432 AAAGTTCGGGATTCAAGATTT-
1 AAGGTTCGAG-TTCAAGATTTA
40272453 AAGGTTC
1 AAGGTTC
40272460 ATGGTTCGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (21 bp):
AAGGTTCGAGTTCAAGATTTA
Found at i:40272726 original size:24 final size:24
Alignment explanation
Indices: 40272648--40272733 Score: 75
Period size: 24 Copynumber: 3.4 Consensus size: 24
40272638 ATAAATAGTG
40272648 TATAATTTAATAAATAAAA-ATTA
1 TATAATTTAATAAATAAAATATTA
* * * *
40272671 TTTAATTTAAATTAAAGGGAAAATGGTAA
1 TATAATTT-AA-TAAA--TAAAAT-ATTA
*
40272700 TATAATTTAATAAATAAAATTTTA
1 TATAATTTAATAAATAAAATATTA
40272724 TATAATTTAA
1 TATAATTTAA
40272734 ATTATTGACT
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
23 7 0.14
24 14 0.29
25 9 0.18
27 8 0.16
28 2 0.04
29 9 0.18
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (24 bp):
TATAATTTAATAAATAAAATATTA
Found at i:40280541 original size:11 final size:11
Alignment explanation
Indices: 40280525--40280552 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
40280515 TTTTAAATAT
40280525 TATTTTCTCCC
1 TATTTTCTCCC
40280536 TATTTTCTCCC
1 TATTTTCTCCC
40280547 TATTTT
1 TATTTT
40280553 GTTGTTATTG
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:0.11, C:0.29, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTTTCTCCC
Found at i:40280651 original size:30 final size:29
Alignment explanation
Indices: 40280594--40280653 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
40280584 ATTTTATTGT
*
40280594 TAATTTTTTATTATTTTAAAGATATTTGC
1 TAATTTTTTATTATTTTAAAGACATTTGC
* * *
40280623 TAATTTTGTTTTTATTTTAGAGGCATTTGC
1 TAATTTT-TTATTATTTTAAAGACATTTGC
40280653 T
1 T
40280654 TGTTAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.25, C:0.05, G:0.12, T:0.58
Consensus pattern (29 bp):
TAATTTTTTATTATTTTAAAGACATTTGC
Found at i:40281290 original size:12 final size:11
Alignment explanation
Indices: 40281271--40281301 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
40281261 TGTATAAAAC
40281271 TTATTTTATTA
1 TTATTTTATTA
40281282 TTAATTTTATTA
1 TT-ATTTTATTA
40281294 TTATTTTA
1 TTATTTTA
40281302 AAGACATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:40281325 original size:30 final size:30
Alignment explanation
Indices: 40281282--40281343 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
40281272 TATTTTATTA
*
40281282 TTAATTTTATTATTATTTTAAAGACATTTG
1 TTAAATTTATTATTATTTTAAAGACATTTG
* * *
40281312 TTAAATTTGTTATTATTTTAGAGGCATTTG
1 TTAAATTTATTATTATTTTAAAGACATTTG
40281342 TT
1 TT
40281344 TGTTAAGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.56
Consensus pattern (30 bp):
TTAAATTTATTATTATTTTAAAGACATTTG
Found at i:40281495 original size:12 final size:12
Alignment explanation
Indices: 40281466--40281497 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
40281456 ATATATTTTT
40281466 AAATT-ATATAA
1 AAATTAATATAA
40281477 AAA-TAATATAA
1 AAATTAATATAA
40281488 AAATTAATAT
1 AAATTAATAT
40281498 GGACAGGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 12 0.63
12 6 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAATTAATATAA
Found at i:40282286 original size:30 final size:31
Alignment explanation
Indices: 40282242--40282316 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
40282232 CAATTTGATA
* ***
40282242 TATATATG-AACTTTGATT-TAGTGCAATTT
1 TATACATGAAACTTTGATTGTAGTGCAAACG
* *
40282271 TATACATGAAACTTTGATTGTGGTTCAAACG
1 TATACATGAAACTTTGATTGTAGTGCAAACG
40282302 TATACATGAAACTTT
1 TATACATGAAACTTT
40282317 AGTTTTGATT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 7 0.18
30 10 0.26
31 21 0.55
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (31 bp):
TATACATGAAACTTTGATTGTAGTGCAAACG
Found at i:40282329 original size:31 final size:31
Alignment explanation
Indices: 40282271--40282329 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
40282261 AGTGCAATTT
*
40282271 TATACATGAAACTTTGATTGTGGTTCAAACG
1 TATACATGAAACTTTGATTGTGATTCAAACG
*
40282302 TATACATGAAACTTT-AGTTTTGATTCAA
1 TATACATGAAACTTTGA-TTGTGATTCAA
40282330 TTATATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (31 bp):
TATACATGAAACTTTGATTGTGATTCAAACG
Found at i:40282937 original size:19 final size:20
Alignment explanation
Indices: 40282915--40282999 Score: 95
Period size: 19 Copynumber: 4.2 Consensus size: 20
40282905 AAAATTACAA
40282915 AAAAATT-AAAATAATTTTT
1 AAAAATTCAAAATAATTTTT
40282934 AAAAATTCAAAATAATTTTT
1 AAAAATTCAAAATAATTTTT
* *
40282954 -AAATTTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTTTT
*
40282972 AAAAATTTCAAAACCTTATTTTT
1 AAAAA-TTCAAAA--TAATTTTT
40282995 AAAAA
1 AAAAA
40283000 AAATTTATAA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
18 5 0.09
19 21 0.38
20 19 0.34
22 1 0.02
23 10 0.18
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTT
Found at i:40282937 original size:20 final size:21
Alignment explanation
Indices: 40282914--40283000 Score: 85
Period size: 20 Copynumber: 4.3 Consensus size: 21
40282904 AAAAATTACA
40282914 AAAAAATT-AAAATAATTTTT
1 AAAAAATTCAAAATAATTTTT
40282934 -AAAAATTCAAAATAATTTTT
1 AAAAAATTCAAAATAATTTTT
* *
40282954 --AAATTTCAAAAT-ATTTAT
1 AAAAAATTCAAAATAATTTTT
* *
40282972 AAAAATTTCAAAACCTTATTTTT
1 AAAAAATTCAAAA--TAATTTTT
40282995 AAAAAA
1 AAAAAA
40283001 AATTTATAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
18 5 0.09
19 18 0.32
20 23 0.40
22 1 0.02
23 10 0.18
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAAATTCAAAATAATTTTT
Found at i:40288291 original size:47 final size:47
Alignment explanation
Indices: 40288204--40288315 Score: 120
Period size: 47 Copynumber: 2.3 Consensus size: 47
40288194 AAACTTAAAT
* *
40288204 CCGTGATCATATAACCACTTTCAACTAGGCTCCTGAGTTATGCTCCAAC
1 CCGTGATCATATAA-C-CTGTCAACTAGGCTCCTGAGTTATACTCCAAC
* * *
40288253 TCGTGACCATATAACCTGTCAACTAGAAGC-CCT-AGTTATACTTCAAC
1 CCGTGATCATATAACCTGTCAACTAG--GCTCCTGAGTTATACTCCAAC
*
40288300 CCGTGATCGTATAACC
1 CCGTGATCATATAACC
40288316 ACCGTAAACT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
47 35 0.66
48 4 0.08
49 14 0.26
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (47 bp):
CCGTGATCATATAACCTGTCAACTAGGCTCCTGAGTTATACTCCAAC
Found at i:40300357 original size:16 final size:17
Alignment explanation
Indices: 40300330--40300362 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
40300320 ATTTAAACTT
40300330 TATTATTTAAAAAATAA
1 TATTATTTAAAAAATAA
40300347 TATTA-TTAAAAAATAA
1 TATTATTTAAAAAATAA
40300363 AATCACGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TATTATTTAAAAAATAA
Found at i:40305271 original size:4 final size:4
Alignment explanation
Indices: 40305262--40305289 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
40305252 AAGGCTCGCT
40305262 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
40305290 ATATAAGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:40310326 original size:46 final size:46
Alignment explanation
Indices: 40310274--40310593 Score: 525
Period size: 46 Copynumber: 7.0 Consensus size: 46
40310264 AGTGTGCTCT
40310274 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
40310320 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
40310366 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
40310412 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
40310458 CTGATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * **
40310504 GTGATATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
40310550 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
40310594 TCATGTCAAA
Statistics
Matches: 260, Mismatches: 13, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
45 1 0.00
46 259 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:40310899 original size:23 final size:25
Alignment explanation
Indices: 40310854--40310900 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
40310844 AATAAATATA
*
40310854 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
40310879 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
40310901 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:40311377 original size:7 final size:7
Alignment explanation
Indices: 40311361--40311996 Score: 315
Period size: 7 Copynumber: 88.3 Consensus size: 7
40311351 AAACCTTATA
*
40311361 AAACCTT
1 AAACCCT
40311368 AAACCCT
1 AAACCCT
*
40311375 AAACCAT
1 AAACCCT
*
40311382 AAACCAT
1 AAACCCT
*
40311389 AAACCTT
1 AAACCCT
**
40311396 GGACCCT
1 AAACCCT
*
40311403 AGACCCT
1 AAACCCT
* *
40311410 AGACCTT
1 AAACCCT
*
40311417 AAACCAT
1 AAACCCT
*
40311424 AAAACACT
1 -AAACCCT
*
40311432 AAAACCT
1 AAACCCT
40311439 AAACCCT
1 AAACCCT
**
40311446 AAAACCAA
1 -AAACCCT
40311454 AAACCCT
1 AAACCCT
*
40311461 AAACTCT
1 AAACCCT
* *
40311468 AAAAGCAT
1 -AAACCCT
40311476 AAACCCT
1 AAACCCT
*
40311483 AAACCCC
1 AAACCCT
40311490 AAACCCAT
1 AAACCC-T
**
40311498 AAACTTT
1 AAACCCT
40311505 AAACCCT
1 AAACCCT
*
40311512 AAA-CTT
1 AAACCCT
*
40311518 AAACCAT
1 AAACCCT
*
40311525 GAAACCAT
1 -AAACCCT
*
40311533 AAACCAT
1 AAACCCT
*
40311540 AAACCTT
1 AAACCCT
*
40311547 AAACACT
1 AAACCCT
40311554 AAACCCT
1 AAACCCT
40311561 AAACCCT
1 AAACCCT
*
40311568 -AAGCC-
1 AAACCCT
40311573 AAA-CCT
1 AAACCCT
* *
40311579 TAACCAT
1 AAACCCT
*
40311586 AAACCAT
1 AAACCCT
*
40311593 AAATCCT
1 AAACCCT
*
40311600 AAACCTT
1 AAACCCT
*
40311607 AAACCTT
1 AAACCCT
*
40311614 AAACCCAA
1 AAACCC-T
*
40311622 AAACACT
1 AAACCCT
*
40311629 AAACCAT
1 AAACCCT
*
40311636 AAAACCT
1 AAACCCT
*
40311643 AAAAACACT
1 --AAACCCT
*
40311652 AAACTCT
1 AAACCCT
*
40311659 AAACCAT
1 AAACCCT
40311666 AAACCCT
1 AAACCCT
*
40311673 AAAACCTT
1 -AAACCCT
*
40311681 AAACCAT
1 AAACCCT
*
40311688 -TACCCT
1 AAACCCT
40311694 AAACCAC-
1 AAACC-CT
*
40311701 AAACCAT
1 AAACCCT
40311708 AAACCCT
1 AAACCCT
*
40311715 AAACTCT
1 AAACCCT
*
40311722 AAACCAT
1 AAACCCT
40311729 AAACCCT
1 AAACCCT
*
40311736 AAAACCTT
1 -AAACCCT
*
40311744 AAACCAT
1 AAACCCT
*
40311751 -TACCCT
1 AAACCCT
40311757 AAACCAC-
1 AAACC-CT
*
40311764 AAACCAT
1 AAACCCT
40311771 AAACCCT
1 AAACCCT
*
40311778 AAACTCT
1 AAACCCT
*
40311785 AAACCAT
1 AAACCCT
40311792 AAACCCT
1 AAACCCT
*
40311799 AAAACCTT
1 -AAACCCT
*
40311807 AAACCAT
1 AAACCCT
*
40311814 -TACCCT
1 AAACCCT
40311820 AAACCAC-
1 AAACC-CT
40311827 AAACCAC-
1 AAACC-CT
*
40311834 AAACCAT
1 AAACCCT
40311841 AAACCCT
1 AAACCCT
40311848 AAACCCT
1 AAACCCT
40311855 AAACCCT
1 AAACCCT
*
40311862 AAAAACCTT
1 --AAACCCT
40311871 AAACCTCAT
1 AAACC-C-T
*
40311880 AAAACC-
1 AAACCCT
40311886 ATAACCCAT
1 A-AACCC-T
40311895 AAACCCT
1 AAACCCT
*
40311902 AAATCCT
1 AAACCCT
40311909 AAACCTCAT
1 AAACC-C-T
* *
40311918 AAAGACAT
1 AAA-CCCT
40311926 AAACCCT
1 AAACCCT
40311933 AAACCCTAT
1 AAACCC--T
**
40311942 AAAATACT
1 -AAACCCT
40311950 AAACCCT
1 AAACCCT
*
40311957 AAACCATAT
1 AAACC--CT
**
40311966 AAAACTTT
1 -AAACCCT
40311974 AAACCCT
1 AAACCCT
*
40311981 AAAACCT
1 AAACCCT
40311988 AAACCCT
1 AAACCCT
40311995 AA
1 AA
40311997 CTTAGTTGCG
Statistics
Matches: 480, Mismatches: 109, Indels: 80
0.72 0.16 0.12
Matches are distributed among these distances:
5 2 0.00
6 26 0.05
7 356 0.74
8 64 0.13
9 23 0.05
10 9 0.02
ACGTcount: A:0.49, C:0.33, G:0.01, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:40311441 original size:15 final size:15
Alignment explanation
Indices: 40311417--40311485 Score: 54
Period size: 15 Copynumber: 4.6 Consensus size: 15
40311407 CCTAGACCTT
40311417 AAACCATAAAACACTA
1 AAACC-TAAAACACTA
*
40311433 AAACCT-AAACCCTA
1 AAACCTAAAACACTA
* *
40311447 AAACCAAAAACCCT-
1 AAACCTAAAACACTA
40311461 AAACTCTAAAAGCA-TA
1 AAAC-CTAAAA-CACTA
*
40311477 AACCCTAAA
1 AAACCTAAA
40311486 CCCCAAACCC
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
14 16 0.36
15 19 0.43
16 9 0.20
ACGTcount: A:0.57, C:0.29, G:0.01, T:0.13
Consensus pattern (15 bp):
AAACCTAAAACACTA
Found at i:40311441 original size:22 final size:21
Alignment explanation
Indices: 40311416--40311487 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 21
40311406 CCCTAGACCT
40311416 TAAACCATAAAACACTAAAACC
1 TAAACC-TAAAACACTAAAACC
*
40311438 TAAACCCTAAAAC-CAAAAACCC
1 TAAA-CCTAAAACACTAAAA-CC
*
40311460 TAAACTCTAAAAGCA-TAAACCC
1 TAAAC-CTAAAA-CACTAAAACC
40311482 TAAACC
1 TAAACC
40311488 CCAAACCCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
21 7 0.17
22 29 0.69
23 6 0.14
ACGTcount: A:0.54, C:0.31, G:0.01, T:0.14
Consensus pattern (21 bp):
TAAACCTAAAACACTAAAACC
Found at i:40311724 original size:63 final size:63
Alignment explanation
Indices: 40311627--40311875 Score: 408
Period size: 63 Copynumber: 3.9 Consensus size: 63
40311617 CCCAAAAACA
* * *
40311627 CTAAACCATAAAACCTAAAAACACTAAACTCTAAACCATAAACCCTAAAACCTTAAACCATTACC
1 CTAAACCA-CAAACC-ATAAACCCTAAACTCTAAACCATAAACCCTAAAACCTTAAACCATTACC
40311692 CTAAACCACAAACCATAAACCCTAAACTCTAAACCATAAACCCTAAAACCTTAAACCATTACC
1 CTAAACCACAAACCATAAACCCTAAACTCTAAACCATAAACCCTAAAACCTTAAACCATTACC
40311755 CTAAACCACAAACCATAAACCCTAAACTCTAAACCATAAACCCTAAAACCTTAAACCATTACC
1 CTAAACCACAAACCATAAACCCTAAACTCTAAACCATAAACCCTAAAACCTTAAACCATTACC
* * * *
40311818 CTAAACCACAAACCACAAACCATAAACCCTAAACCCTAAACCCTAAAAACCTTAAACC
1 CTAAACCACAAACCATAAACCCTAAACTCTAAACCATAAACCCT-AAAACCTTAAACC
40311876 TCATAAAACC
Statistics
Matches: 176, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
63 150 0.85
64 18 0.10
65 8 0.05
ACGTcount: A:0.49, C:0.35, G:0.00, T:0.16
Consensus pattern (63 bp):
CTAAACCACAAACCATAAACCCTAAACTCTAAACCATAAACCCTAAAACCTTAAACCATTACC
Found at i:40311927 original size:38 final size:39
Alignment explanation
Indices: 40311416--40311940 Score: 189
Period size: 36 Copynumber: 14.4 Consensus size: 39
40311406 CCCTAGACCT
* *
40311416 TAAACCATAAAACACTAAAACC-TAAACC-C-TAAAACCA
1 TAAACCCT-AAACCCTAAAACCTTAAACCTCATAAAACCA
* * * * *
40311453 AAAACCCTAAACTCTAAAAGCATAAACC-C-T-AAACCC
1 TAAACCCTAAACCCTAAAACCTTAAACCTCATAAAACCA
* * * *
40311489 CAAACCCATAAA-CTTTAAACCCTAAA-CT--T-AAACCA
1 TAAACCC-TAAACCCTAAAACCTTAAACCTCATAAAACCA
* * * *
40311524 TGAAACCATAAACCAT-AAACCTTAAA-CAC-T-AAACCC
1 T-AAACCCTAAACCCTAAAACCTTAAACCTCATAAAACCA
*
40311560 TAAACCCT-AAGCC--AAACCTT-AA-C-CAT-AAACCA
1 TAAACCCTAAACCCTAAAACCTTAAACCTCATAAAACCA
* *
40311592 TAAATCCTAAA-CCTTAAACCTTAAACC-CA-AAAA-CA
1 TAAACCCTAAACCCTAAAACCTTAAACCTCATAAAACCA
* *
40311627 CTAAACCATAAAACCTAAAAACAC-TAAA-CTC-T-AAACCA
1 -TAAACCCTAAACCCT-AAAAC-CTTAAACCTCATAAAACCA
* * * * *
40311665 TAAACCCTAAAACCTTAAACCATT-ACCCTAAACCACAAACCA
1 TAAACCCTAAACCCTAAAACC-TTAAACCT-CA-TA-AAACCA
* * *
40311707 TAAACCCTAAACTCT-AAACCATAAACC-C-TAAAACCT
1 TAAACCCTAAACCCTAAAACCTTAAACCTCATAAAACCA
* * ** *
40311743 TAAACCAT-TACCCT-AAACCACAAA-C-CAT-AAACCC
1 TAAACCCTAAACCCTAAAACCTTAAACCTCATAAAACCA
* * * *
40311777 TAAACTCTAAACCATAAACCCTAAAACCT--T-AAACCA
1 TAAACCCTAAACCCTAAAACCTTAAACCTCATAAAACCA
* ** *
40311813 T-TACCCTAAA-CC-ACAAACCACAAA-C-CAT-AAACCC
1 TAAACCCTAAACCCTA-AAACCTTAAACCTCATAAAACCA
40311847 TAAACCCTAAACCCTAAAAACCTTAAACCTCATAAAACCA
1 TAAACCCTAAACCCT-AAAACCTTAAACCTCATAAAACCA
*
40311887 T-AACCCATAAACCCTAAATCC-TAAACCTCATAAAGA-CA
1 TAAACCC-TAAACCCTAAAACCTTAAACCTCATAAA-ACCA
40311925 TAAACCCTAAACCCTA
1 TAAACCCTAAACCCTA
40311941 TAAAATACTA
Statistics
Matches: 378, Mismatches: 63, Indels: 93
0.71 0.12 0.17
Matches are distributed among these distances:
31 1 0.00
32 18 0.05
33 11 0.03
34 38 0.10
35 65 0.17
36 93 0.25
37 52 0.14
38 38 0.10
39 20 0.05
40 15 0.04
41 8 0.02
42 19 0.05
ACGTcount: A:0.50, C:0.33, G:0.01, T:0.17
Consensus pattern (39 bp):
TAAACCCTAAACCCTAAAACCTTAAACCTCATAAAACCA
Found at i:40311952 original size:24 final size:24
Alignment explanation
Indices: 40311900--40311988 Score: 85
Period size: 24 Copynumber: 3.7 Consensus size: 24
40311890 CCCATAAACC
* *
40311900 CTAAATCCTAAA-CCTCAT-AAAGA
1 CTAAACCCTAAACCCT-ATAAAATA
40311923 CATAAACCCTAAACCCTATAAAATA
1 C-TAAACCCTAAACCCTATAAAATA
*
40311948 CTAAACCCTAAACCATATAAAACT-
1 CTAAACCCTAAACCCTATAAAA-TA
* *
40311972 TTAAACCCTAAAACCTA
1 CTAAACCCTAAACCCTA
40311989 AACCCTAACT
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
23 1 0.02
24 46 0.82
25 9 0.16
ACGTcount: A:0.49, C:0.28, G:0.01, T:0.21
Consensus pattern (24 bp):
CTAAACCCTAAACCCTATAAAATA
Found at i:40319129 original size:93 final size:93
Alignment explanation
Indices: 40319022--40319192 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
40319012 GCCCCTAAGT
* *
40319022 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40319087 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
40319115 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40319180 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40319193 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40319189 original size:46 final size:46
Alignment explanation
Indices: 40319017--40319189 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
40319007 AACCCGCCCC
* * *
40319017 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
40319063 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
40319111 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
40319156 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40319190 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:40319646 original size:30 final size:30
Alignment explanation
Indices: 40319612--40319671 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
40319602 ATTTAATACG
40319612 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
40319642 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
40319672 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:40322720 original size:43 final size:42
Alignment explanation
Indices: 40322639--40322720 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 42
40322629 CTAGGACATC
* **
40322639 GACATCGTATTTAATTTCATGTAAGACCCTATTTGGGACAAT
1 GACATCGTATTTAATTACATGTAAGACCCTATCCGGGACAAT
*
40322681 GACATCGATATTTGATTACATGTAAGACCAC-ATCCGGGAC
1 GACATCG-TATTTAATTACATGTAAGACC-CTATCCGGGAC
40322721 GTTGGCATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 7 0.21
43 26 0.76
44 1 0.03
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (42 bp):
GACATCGTATTTAATTACATGTAAGACCCTATCCGGGACAAT
Found at i:40325461 original size:15 final size:15
Alignment explanation
Indices: 40325441--40325498 Score: 59
Period size: 15 Copynumber: 4.0 Consensus size: 15
40325431 GTTTGAAAAA
40325441 TTGAAAAATTAAATG
1 TTGAAAAATTAAATG
*
40325456 TTG-AAAA-TAAGTG
1 TTGAAAAATTAAATG
* *
40325469 TTGAAAAAATAAATA
1 TTGAAAAATTAAATG
40325484 TT-AAAAATCTAAATG
1 TTGAAAAAT-TAAATG
40325499 ATGGACTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 8 0.23
14 13 0.37
15 14 0.40
ACGTcount: A:0.55, C:0.02, G:0.12, T:0.31
Consensus pattern (15 bp):
TTGAAAAATTAAATG
Found at i:40334183 original size:17 final size:17
Alignment explanation
Indices: 40334161--40334243 Score: 63
Period size: 17 Copynumber: 5.1 Consensus size: 17
40334151 ATGTTTTTCC
40334161 ATAAAAAATATTTAAAA
1 ATAAAAAATATTTAAAA
*
40334178 ATAAAAAATA--T---C
1 ATAAAAAATATTTAAAA
*
40334190 ATAAAAAATTTTTAAAA
1 ATAAAAAATATTTAAAA
*
40334207 TATAAAAAGTATTTAAAA
1 -ATAAAAAATATTTAAAA
40334225 A-ACATAAAAT-TTTAAAA
1 ATA-A-AAAATATTTAAAA
40334242 AT
1 AT
40334244 TCTAAGAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
12 9 0.18
14 1 0.02
15 1 0.02
16 1 0.02
17 20 0.39
18 19 0.37
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.31
Consensus pattern (17 bp):
ATAAAAAATATTTAAAA
Found at i:40334211 original size:18 final size:18
Alignment explanation
Indices: 40334190--40334243 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
40334180 AAAAAATATC
40334190 ATAAAAAATTTTTAAAAT
1 ATAAAAAATTTTTAAAAT
* * *
40334208 ATAAAAAGTATTTAAAAA
1 ATAAAAAATTTTTAAAAT
* * *
40334226 ACATAAAATTTTAAAAAT
1 ATAAAAAATTTTTAAAAT
40334244 TCTAAGAAAT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
ATAAAAAATTTTTAAAAT
Found at i:40334226 original size:30 final size:29
Alignment explanation
Indices: 40334160--40334297 Score: 92
Period size: 29 Copynumber: 4.9 Consensus size: 29
40334150 AATGTTTTTC
40334160 CATAAAAAATATTTAAAAATAAAAAATAT
1 CATAAAAAATATTTAAAAATAAAAAATAT
* *
40334189 CATAAAAAATTTTTAAAATATAAAAAGTAT
1 CATAAAAAATATTTAAAA-ATAAAAAATAT
* * * *
40334219 -TTAAAAAACA--TAAAATTTTAAAAAT-T
1 CATAAAAAATATTTAAAA-ATAAAAAATAT
* * *
40334245 C-TAAGAAAT-TATAAAAAATATAAAAT-T
1 CATAAAAAATAT-TTAAAAATAAAAAATAT
** *
40334272 CATAAAACTTATTTAAAATTAAAAAA
1 CATAAAAAATATTTAAAAATAAAAAA
40334298 AAACATATTG
Statistics
Matches: 82, Mismatches: 20, Indels: 15
0.70 0.17 0.13
Matches are distributed among these distances:
26 7 0.09
27 20 0.24
28 20 0.24
29 25 0.30
30 10 0.12
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (29 bp):
CATAAAAAATATTTAAAAATAAAAAATAT
Found at i:40334242 original size:9 final size:9
Alignment explanation
Indices: 40334230--40334297 Score: 50
Period size: 10 Copynumber: 7.4 Consensus size: 9
40334220 TAAAAAACAT
*
40334230 AAAATTTTA
1 AAAATTATA
*
40334239 AAAATTCTA
1 AAAATTATA
40334248 AGAAATTATA
1 A-AAATTATA
*
40334258 AAAAATAT-
1 AAAATTATA
40334266 AAAATTCATA
1 AAAATT-ATA
* *
40334276 AAACTTATTT
1 AAAATTA-TA
40334286 AAAATTA-A
1 AAAATTATA
40334294 AAAA
1 AAAA
40334298 AAACATATTG
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
8 9 0.19
9 18 0.38
10 20 0.43
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (9 bp):
AAAATTATA
Found at i:40334296 original size:27 final size:26
Alignment explanation
Indices: 40334236--40334296 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
40334226 ACATAAAATT
40334236 TTAAAAATTCTAAGAAATTATAAAAA
1 TTAAAAATTCTAAGAAATTATAAAAA
* * *
40334262 ATATAAAATTCATAA-AACTTATTTAAAA
1 TTA-AAAATTC-TAAGAAATTA-TAAAAA
40334290 TTAAAAA
1 TTAAAAA
40334297 AAAACATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
26 2 0.07
27 16 0.57
28 10 0.36
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.33
Consensus pattern (26 bp):
TTAAAAATTCTAAGAAATTATAAAAA
Found at i:40334809 original size:12 final size:12
Alignment explanation
Indices: 40334792--40334817 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40334782 CCACTTCAAG
40334792 TTTTTATAATTT
1 TTTTTATAATTT
40334804 TTTTTATAATTT
1 TTTTTATAATTT
40334816 TT
1 TT
40334818 ATAAGCTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTATAATTT
Found at i:40334816 original size:9 final size:9
Alignment explanation
Indices: 40334804--40334894 Score: 55
Period size: 9 Copynumber: 10.0 Consensus size: 9
40334794 TTTATAATTT
40334804 TTTTTATAA
1 TTTTTATAA
40334813 TTTTTATAA
1 TTTTTATAA
* *
40334822 GCTTATATCAA
1 -TTTTTAT-AA
* *
40334833 CTTTAATAA
1 TTTTTATAA
*
40334842 GTTTT-T--
1 TTTTTATAA
40334848 TT-TTATAA
1 TTTTTATAA
*
40334856 TTTTTATGA
1 TTTTTATAA
40334865 TTTTTATAGA
1 TTTTTATA-A
40334875 TTTTTAATACA
1 TTTTT-ATA-A
40334886 TTTTTATAA
1 TTTTTATAA
40334895 AGGTTTAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
5 2 0.03
6 2 0.03
8 3 0.05
9 27 0.42
10 19 0.30
11 11 0.17
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.59
Consensus pattern (9 bp):
TTTTTATAA
Found at i:40334880 original size:10 final size:10
Alignment explanation
Indices: 40334847--40334893 Score: 62
Period size: 9 Copynumber: 4.8 Consensus size: 10
40334837 AATAAGTTTT
40334847 TTTTTATA-A
1 TTTTTATAGA
40334856 TTTTTAT-GA
1 TTTTTATAGA
40334865 TTTTTATAGA
1 TTTTTATAGA
*
40334875 TTTTTAATACA
1 TTTTT-ATAGA
40334886 TTTTTATA
1 TTTTTATA
40334894 AAGGTTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
9 15 0.44
10 10 0.29
11 9 0.26
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (10 bp):
TTTTTATAGA
Found at i:40335013 original size:20 final size:21
Alignment explanation
Indices: 40334990--40335037 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
40334980 TTTTTAAATA
40334990 TTTAATAGTATTTAT-ATTTT
1 TTTAATAGTATTTATGATTTT
*
40335010 TTT-ATAATTATTTATGATTTT
1 TTTAAT-AGTATTTATGATTTT
*
40335031 TTAAATA
1 TTTAATA
40335038 AATTTTATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 2 0.09
20 11 0.48
21 8 0.35
22 2 0.09
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTAATAGTATTTATGATTTT
Found at i:40341647 original size:27 final size:26
Alignment explanation
Indices: 40341586--40341648 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
40341576 ACTTTATTTT
40341586 ATTTATATTAGGATCATTAATATTAAG
1 ATTT-TATTAGGATCATTAATATTAAG
* * * *
40341613 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGATCA-TTAATATTAAG
40341641 ATTTTATT
1 ATTTTATT
40341649 TTAATTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.51
Consensus pattern (26 bp):
ATTTTATTAGGATCATTAATATTAAG
Found at i:40344836 original size:17 final size:19
Alignment explanation
Indices: 40344793--40344828 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40344783 GCACAATGAT
*
40344793 TGTTCAAGTGTCAGATTTG
1 TGTTTAAGTGTCAGATTTG
40344812 TGTTTAAGTGTCA-ATTT
1 TGTTTAAGTGTCAGATTT
40344829 TTTTTAAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.47
Consensus pattern (19 bp):
TGTTTAAGTGTCAGATTTG
Found at i:40349828 original size:18 final size:18
Alignment explanation
Indices: 40349805--40349842 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40349795 ATAGGCTCAC
*
40349805 TATTCACCTAAACCCAAT
1 TATTCAACTAAACCCAAT
*
40349823 TATTCAACTCAACCCAAT
1 TATTCAACTAAACCCAAT
40349841 TA
1 TA
40349843 CCCAACCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (18 bp):
TATTCAACTAAACCCAAT
Found at i:40349848 original size:18 final size:18
Alignment explanation
Indices: 40349815--40349858 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
40349805 TATTCACCTA
** *
40349815 AACCCAATTATTCAACTC
1 AACCCAATTACCCAACCC
40349833 AACCCAATTACCCAACCC
1 AACCCAATTACCCAACCC
40349851 AACCCAAT
1 AACCCAAT
40349859 CATAAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.18
Consensus pattern (18 bp):
AACCCAATTACCCAACCC
Found at i:40350012 original size:9 final size:9
Alignment explanation
Indices: 40349964--40350032 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
40349954 TGTAGTGATT
40349964 TAATTT-GA
1 TAATTTGGA
* *
40349972 TTAATTCGGT
1 -TAATTTGGA
40349982 TAATTTGGA
1 TAATTTGGA
*
40349991 TAA-TTCGA
1 TAATTTGGA
40349999 TTAATTTGGA
1 -TAATTTGGA
*
40350009 TAATTCGGA
1 TAATTTGGA
* *
40350018 TAATTCGGT
1 TAATTTGGA
40350027 TAATTT
1 TAATTT
40350033 TTAACCAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
8 4 0.08
9 39 0.81
10 5 0.10
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.46
Consensus pattern (9 bp):
TAATTTGGA
Found at i:40350031 original size:18 final size:18
Alignment explanation
Indices: 40349963--40350022 Score: 86
Period size: 18 Copynumber: 3.3 Consensus size: 18
40349953 ATGTAGTGAT
40349963 TTAATTT-GATTAATTCGG
1 TTAATTTGGA-TAATTCGG
*
40349981 TTAATTTGGATAATTCGA
1 TTAATTTGGATAATTCGG
40349999 TTAATTTGGATAATTCGG
1 TTAATTTGGATAATTCGG
*
40350017 ATAATT
1 TTAATT
40350023 CGGTTAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 36 0.95
19 2 0.05
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.47
Consensus pattern (18 bp):
TTAATTTGGATAATTCGG
Found at i:40350032 original size:27 final size:27
Alignment explanation
Indices: 40349964--40350032 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
40349954 TGTAGTGATT
* * * *
40349964 TAATTTGATTAATTCGGTTAATTTGGA
1 TAATTCGATTAATTTGGATAATTCGGA
40349991 TAATTCGATTAATTTGGATAATTCGGA
1 TAATTCGATTAATTTGGATAATTCGGA
*
40350018 TAATTCGGTTAATTT
1 TAATTCGATTAATTT
40350033 TTAACCAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.46
Consensus pattern (27 bp):
TAATTCGATTAATTTGGATAATTCGGA
Found at i:40350212 original size:12 final size:12
Alignment explanation
Indices: 40350195--40350219 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40350185 TGTTATTTCG
40350195 GGTCGGTTAACC
1 GGTCGGTTAACC
40350207 GGTCGGTTAACC
1 GGTCGGTTAACC
40350219 G
1 G
40350220 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:40354092 original size:231 final size:231
Alignment explanation
Indices: 40353689--40354847 Score: 2318
Period size: 231 Copynumber: 5.0 Consensus size: 231
40353679 ATGGTAGCAA
40353689 AATTGTCATCAGCTAAAACCATATCTGAAGCGCTCTGTATTTGGAAGAATAAAGATAAAGAGAAT
1 AATTGTCATCAGCTAAAACCATATCTGAAGCGCTCTGTATTTGGAAGAATAAAGATAAAGAGAAT
40353754 GAAGAAAACCAAAGAGCATTACTCTTCAAATAACATCAAAGTGAACATATATCAAACAAAATGAG
66 GAAGAAAACCAAAGAGCATTACTCTTCAAATAACATCAAAGTGAACATATATCAAACAAAATGAG
40353819 AGCATCATGGCTAAAAGGATTATGGTTTTAAAAGCCAGTAACGTAGAAAGTAGATATCATTGTGT
131 AGCATCATGGCTAAAAGGATTATGGTTTTAAAAGCCAGTAACGTAGAAAGTAGATATCATTGTGT
40353884 CATTAGAATGCATAGTTGTTTTTATATTGGTTATAC
196 CATTAGAATGCATAGTTGTTTTTATATTGGTTATAC
40353920 AATTGTCATCAGCTAAAACCATATCTGAAGCGCTCTGTATTTGGAAGAATAAAGATAAAGAGAAT
1 AATTGTCATCAGCTAAAACCATATCTGAAGCGCTCTGTATTTGGAAGAATAAAGATAAAGAGAAT
40353985 GAAGAAAACCAAAGAGCATTACTCTTCAAATAACATCAAAGTGAACATATATCAAACAAAATGAG
66 GAAGAAAACCAAAGAGCATTACTCTTCAAATAACATCAAAGTGAACATATATCAAACAAAATGAG
40354050 AGCATCATGGCTAAAAGGATTATGGTTTTAAAAGCCAGTAACGTAGAAAGTAGATATCATTGTGT
131 AGCATCATGGCTAAAAGGATTATGGTTTTAAAAGCCAGTAACGTAGAAAGTAGATATCATTGTGT
40354115 CATTAGAATGCATAGTTGTTTTTATATTGGTTATAC
196 CATTAGAATGCATAGTTGTTTTTATATTGGTTATAC
40354151 AATTGTCATCAGCTAAAACCATATCTGAAGCGCTCTGTATTTGGAAGAATAAAGATAAAGAGAAT
1 AATTGTCATCAGCTAAAACCATATCTGAAGCGCTCTGTATTTGGAAGAATAAAGATAAAGAGAAT
40354216 GAAGAAAACCAAAGAGCATTACTCTTCAAATAACATCAAAGTGAACATATATCAAACAAAATGAG
66 GAAGAAAACCAAAGAGCATTACTCTTCAAATAACATCAAAGTGAACATATATCAAACAAAATGAG
40354281 AGCATCATGGCTAAAAGGATTATGGTTTTAAAAGCCAGTAACGTAGAAAGTAGATATCATTGTGT
131 AGCATCATGGCTAAAAGGATTATGGTTTTAAAAGCCAGTAACGTAGAAAGTAGATATCATTGTGT
40354346 CATTAGAATGCATAGTTGTTTTTATATTGGTTATAC
196 CATTAGAATGCATAGTTGTTTTTATATTGGTTATAC
40354382 AATTGTCATCAGCTAAAACCATATCTGAAGCGCTCTGTATTTGGAAGAATAAAGATAAAGAGAAT
1 AATTGTCATCAGCTAAAACCATATCTGAAGCGCTCTGTATTTGGAAGAATAAAGATAAAGAGAAT
40354447 GAAGAAAACCAAAGAGCATTACTCTTCAAATAACATCAAAGTGAACATATATCAAACAAAATGAG
66 GAAGAAAACCAAAGAGCATTACTCTTCAAATAACATCAAAGTGAACATATATCAAACAAAATGAG
40354512 AGCATCATGGCTAAAAGGATTATGGTTTTAAAAGCCAGTAACGTAGAAAGTAGATATCATTGTGT
131 AGCATCATGGCTAAAAGGATTATGGTTTTAAAAGCCAGTAACGTAGAAAGTAGATATCATTGTGT
40354577 CATTAGAATGCATAGTTGTTTTTATATTGGTTATAC
196 CATTAGAATGCATAGTTGTTTTTATATTGGTTATAC
40354613 AATTGTCATCAGCTAAAACCATATCTGAAGCGCTCTGTATTTGGAAGAATAAAGATAAAGAGAAT
1 AATTGTCATCAGCTAAAACCATATCTGAAGCGCTCTGTATTTGGAAGAATAAAGATAAAGAGAAT
40354678 GAAGAAAACCAAAGAGCATTACTCTTCAAATAACATCAAAGTGAACATATATCAAACAAAATGAG
66 GAAGAAAACCAAAGAGCATTACTCTTCAAATAACATCAAAGTGAACATATATCAAACAAAATGAG
40354743 AGCATCATGGCTAAAAGGATTATGGTTTTAAAAGCCAGTAACGTAGAAAGTAGATATCATTGTGT
131 AGCATCATGGCTAAAAGGATTATGGTTTTAAAAGCCAGTAACGTAGAAAGTAGATATCATTGTGT
40354808 CATTAGAATGCATAGTTGTTTTTATATTGGTTATAC
196 CATTAGAATGCATAGTTGTTTTTATATTGGTTATAC
40354844 AATT
1 AATT
40354848 TTTATAAAAT
Statistics
Matches: 928, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
231 928 1.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (231 bp):
AATTGTCATCAGCTAAAACCATATCTGAAGCGCTCTGTATTTGGAAGAATAAAGATAAAGAGAAT
GAAGAAAACCAAAGAGCATTACTCTTCAAATAACATCAAAGTGAACATATATCAAACAAAATGAG
AGCATCATGGCTAAAAGGATTATGGTTTTAAAAGCCAGTAACGTAGAAAGTAGATATCATTGTGT
CATTAGAATGCATAGTTGTTTTTATATTGGTTATAC
Found at i:40367253 original size:20 final size:21
Alignment explanation
Indices: 40367218--40367256 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
40367208 AATTAAAAAT
*
40367218 CCAAATTATTTTTTTAAAGAG
1 CCAAATTATATTTTTAAAGAG
40367239 CCAAATTA-ATTTTTAAAG
1 CCAAATTATATTTTTAAAG
40367257 TAGAAGTCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (21 bp):
CCAAATTATATTTTTAAAGAG
Found at i:40370309 original size:14 final size:14
Alignment explanation
Indices: 40370292--40370318 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40370282 AATGAAATTG
40370292 AAAATGAAAAATAA
1 AAAATGAAAAATAA
40370306 AAAATGAAAAATA
1 AAAATGAAAAATA
40370319 CCTAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (14 bp):
AAAATGAAAAATAA
Found at i:40377494 original size:17 final size:17
Alignment explanation
Indices: 40377472--40377505 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40377462 ATCCACTAAT
*
40377472 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
40377489 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
40377506 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:40380683 original size:17 final size:17
Alignment explanation
Indices: 40380661--40380694 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40380651 ATCCACTAAT
*
40380661 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
40380678 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
40380695 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:40411587 original size:30 final size:32
Alignment explanation
Indices: 40411552--40411622 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 32
40411542 CAAATTTATT
* *
40411552 AATTTTTTTAATATTAGA-ACTAAA-ATGATA
1 AATTTTTTAAATATTAAAGACTAAATATGATA
* * *
40411582 AATTTTGTAAATATTAAAGACTAAATTTGTTA
1 AATTTTTTAAATATTAAAGACTAAATATGATA
40411614 AATTTTTTA
1 AATTTTTTA
40411623 TATTTAAGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 15 0.45
31 6 0.18
32 12 0.36
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (32 bp):
AATTTTTTAAATATTAAAGACTAAATATGATA
Found at i:40411626 original size:30 final size:30
Alignment explanation
Indices: 40411543--40411638 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
40411533 GTTGCTAGCC
* * *
40411543 AAATTTATTAATTTTTTTAATATTAGA-ACT
1 AAATTTGTTAAATTTTTT-ATATTAAAGACT
* * *
40411573 AAA-ATGATAAATTTTGTAAATATTAAAGACT
1 AAATTTGTTAAATTTT-T-TATATTAAAGACT
* *
40411604 AAATTTGTTAAATTTTTTATATTTAAGATT
1 AAATTTGTTAAATTTTTTATATTAAAGACT
40411634 AAATT
1 AAATT
40411639 AATAGAATGA
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
29 8 0.16
30 26 0.51
31 7 0.14
32 10 0.20
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (30 bp):
AAATTTGTTAAATTTTTTATATTAAAGACT
Done.