Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 153 of 444
Found at i:41508616 original size:24 final size:24
Alignment explanation
Indices: 41508589--41508637 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
41508579 CATATATTTA
41508589 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTTTATATAAAAATTAAT
41508613 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTTTATATAAAAATTAAT
41508637 T
1 T
41508638 GTTATTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
TTAAAAGTTTATATAAAAATTAAT
Found at i:41509127 original size:19 final size:22
Alignment explanation
Indices: 41509086--41509147 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
41509076 ATGTTAATTT
*
41509086 AAAAATTATAAAAATCTTCAAA
1 AAAAATTATAAAAATCTTAAAA
41509108 AAAAATT-T-AAAAT-TTAAAA
1 AAAAATTATAAAAATCTTAAAA
* *
41509127 ATAAAA-AATAAAAAACTTAAA
1 A-AAAATTATAAAAATCTTAAA
41509148 TATTTAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
19 6 0.18
20 10 0.30
21 5 0.15
22 12 0.36
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAAATTATAAAAATCTTAAAA
Found at i:41509280 original size:8 final size:8
Alignment explanation
Indices: 41509267--41509302 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
41509257 AATTTGAAAG
41509267 AAAAAATA
1 AAAAAATA
41509275 AAAAAATAA
1 AAAAAAT-A
41509284 AAAAAATA
1 AAAAAATA
*
41509292 AAAAATTA
1 AAAAAATA
41509300 AAA
1 AAA
41509303 TTAAACAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 18 0.69
9 8 0.31
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (8 bp):
AAAAAATA
Found at i:41509286 original size:9 final size:9
Alignment explanation
Indices: 41509267--41509296 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
41509257 AATTTGAAAG
41509267 AAAAAAT-A
1 AAAAAATAA
41509275 AAAAAATAA
1 AAAAAATAA
41509284 AAAAAATAA
1 AAAAAATAA
41509293 AAAA
1 AAAA
41509297 TTAAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAATAA
Found at i:41509289 original size:17 final size:17
Alignment explanation
Indices: 41509267--41509302 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
41509257 AATTTGAAAG
41509267 AAAAAATAAAAAAATAA
1 AAAAAATAAAAAAATAA
*
41509284 AAAAAATAAAAAATTAA
1 AAAAAATAAAAAAATAA
41509301 AA
1 AA
41509303 TTAAACAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAAAATAAAAAAATAA
Found at i:41512576 original size:20 final size:20
Alignment explanation
Indices: 41512516--41512577 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
41512506 AAATTTCAAA
*
41512516 AATTAAACATAATATAATATTT
1 AATTAAA-ATAAAAT-ATATTT
*
41512538 AA-CATAAA-AAAATATTATTT
1 AATTA-AAATAAAATA-TATTT
41512558 AATTAAAATAAAATATATTT
1 AATTAAAATAAAATATATTT
41512578 TTTAAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
19 1 0.03
20 19 0.58
21 9 0.27
22 4 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTAAAATAAAATATATTT
Found at i:41512641 original size:43 final size:43
Alignment explanation
Indices: 41512580--41512780 Score: 215
Period size: 43 Copynumber: 4.7 Consensus size: 43
41512570 ATATATTTTT
* * * *** *
41512580 TAAAATTCATGATTTTTAGCGGCGTTTTTGGGAAAAGCGCCTC
1 TAAAAGTCATGGTCTTTAGCGGCGTTTTTAAAAAAAGCGCCGC
*
41512623 TAAAAGTCATGGTCTTTAGCGGCGTTTGTAAAAAAAGCGCCGC
1 TAAAAGTCATGGTCTTTAGCGGCGTTTTTAAAAAAAGCGCCGC
* * ** * *
41512666 TAAAGGTCATGGTCTTTAGTGGCGTTTTT-AGGAAAGTGTCGC
1 TAAAAGTCATGGTCTTTAGCGGCGTTTTTAAAAAAAGCGCCGC
* * * * *
41512708 TAAAGGTCATGGTCTTTAGTGGCGTTTGTAAAAAATGCGCCAC
1 TAAAAGTCATGGTCTTTAGCGGCGTTTTTAAAAAAAGCGCCGC
41512751 TAAAAGTCATGGTCTTTAGCGGCGCTTTTT
1 TAAAAGTCATGGTCTTTAGCGGCG-TTTTT
41512781 TAAATAAACG
Statistics
Matches: 131, Mismatches: 25, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
42 37 0.28
43 90 0.69
44 4 0.03
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (43 bp):
TAAAAGTCATGGTCTTTAGCGGCGTTTTTAAAAAAAGCGCCGC
Found at i:41512726 original size:85 final size:86
Alignment explanation
Indices: 41512580--41512780 Score: 269
Period size: 85 Copynumber: 2.3 Consensus size: 86
41512570 ATATATTTTT
* * * * *
41512580 TAAAATTCATGATTTTTAGCGGCGTTTTTGGGAAAAGCGCCTCTAAAAGTCATGGTCTTTAGCGG
1 TAAAAGTCATGGTCTTTAGCGGCGTTTTTAGGAAAAGCGCCGCTAAAAGTCATGGTCTTTAGCGG
*
41512645 CGTTTGTAAAAAAAGCGCCGC
66 CGTTTGTAAAAAAAGCGCCAC
* * * * * *
41512666 TAAAGGTCATGGTCTTTAGTGGCGTTTTTAGG-AAAGTGTCGCTAAAGGTCATGGTCTTTAGTGG
1 TAAAAGTCATGGTCTTTAGCGGCGTTTTTAGGAAAAGCGCCGCTAAAAGTCATGGTCTTTAGCGG
*
41512730 CGTTTGTAAAAAATGCGCCAC
66 CGTTTGTAAAAAAAGCGCCAC
41512751 TAAAAGTCATGGTCTTTAGCGGCGCTTTTT
1 TAAAAGTCATGGTCTTTAGCGGCG-TTTTT
41512781 TAAATAAACG
Statistics
Matches: 99, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
85 68 0.69
86 31 0.31
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (86 bp):
TAAAAGTCATGGTCTTTAGCGGCGTTTTTAGGAAAAGCGCCGCTAAAAGTCATGGTCTTTAGCGG
CGTTTGTAAAAAAAGCGCCAC
Found at i:41514747 original size:19 final size:19
Alignment explanation
Indices: 41514707--41514758 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 19
41514697 TCAACCTTTA
41514707 AATCAAGTTAAAATGGTTTC
1 AATCAAGTTAAAAT-GTTTC
41514727 AATCAAGTTAGAAAT-TTTC
1 AATCAAGTTA-AAATGTTTC
41514746 AATCAAAGTTAAA
1 AATC-AAGTTAAA
41514759 CTATTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.33
20 16 0.53
21 4 0.13
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.33
Consensus pattern (19 bp):
AATCAAGTTAAAATGTTTC
Found at i:41516998 original size:40 final size:41
Alignment explanation
Indices: 41516943--41517110 Score: 175
Period size: 40 Copynumber: 4.2 Consensus size: 41
41516933 TGAATGATAC
* *
41516943 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCTGATTATAT
* * *
41516983 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCTGATTATAT
* * ** *
41517023 CTGGGCTAAGACCCGAAGGCATTTGTGCAAGCT-ACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCTGATTATAT
* * * *
41517063 CCGGGTTAAGACCCGAAGGCAATTGTGCTTG-TGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCTGATTATAT
41517103 CC-GGCTAA
1 CCGGGCTAA
41517111 ATTCCGAAGA
Statistics
Matches: 104, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
39 6 0.06
40 96 0.92
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (41 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCTGATTATAT
Found at i:41517100 original size:80 final size:80
Alignment explanation
Indices: 41516945--41517103 Score: 196
Period size: 80 Copynumber: 2.0 Consensus size: 80
41516935 AATGATACCC
* * ** *
41516945 GGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCATTCGTG
1 GGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGCATTCGTG
*
41517010 CGAGTTGTTATATCT
66 CGAGTGGTTATATCT
* *
41517025 GGGCTAAGACCCGAAGGCATTTGTGCAAGCT-ACCAAATCCGGGTTAAGACCCGAAGGCAATT-G
1 GGGCTAAGACCCGAAGGCATTTATGCAAG-TGACCAAATCCGGGCTAAGACCCGAAGGC-ATTCG
**
41517088 TGCTTGTGGTTATATC
64 TGCGAGTGGTTATATC
41517104 CGGCTAAATT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
80 63 0.94
81 4 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
GGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGCATTCGTG
CGAGTGGTTATATCT
Found at i:41520245 original size:20 final size:20
Alignment explanation
Indices: 41520220--41520290 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
41520210 CGTGATTTGG
41520220 TATCGATACCATTTTAAAAT
1 TATCGATACCATTTTAAAAT
*
41520240 TATCGATA-TATTTATAAAAT
1 TATCGATACCATTT-TAAAAT
* * * *
41520260 TATCAATACCCTCTTAAAAAA
1 TATCGATACCAT-TTTAAAAT
41520281 TATCGATACC
1 TATCGATACC
41520291 TATCGGGTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
19 4 0.10
20 21 0.51
21 14 0.34
22 2 0.05
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.37
Consensus pattern (20 bp):
TATCGATACCATTTTAAAAT
Found at i:41523692 original size:23 final size:21
Alignment explanation
Indices: 41523640--41523735 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
41523630 CCTGATCAGT
** * *
41523640 ATACGACACATAAAGTGCCTA
1 ATACGACACACGAGGTGCCTG
*
41523661 AAACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
41523682 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
41523703 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
41523724 AAATACGACACA
1 --ATACGACACA
41523736 TAAAGTGCCT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
21 57 0.85
23 10 0.15
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTG
Found at i:41523700 original size:42 final size:43
Alignment explanation
Indices: 41523640--41523745 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 43
41523630 CCTGATCAGT
*
41523640 ATACGACACATAAAGTGCCTAAAACGACACACGAGGTGCCTG-
1 ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTGA
* * * *
41523682 ATACGACACACGAGGTGCCTGATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTG-A
*
41523726 ATACGACACATAAAGTGCCT
1 ATACGACACACAAAGTGCCT
41523746 GATCGATAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 37 0.69
44 17 0.31
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (43 bp):
ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTGA
Found at i:41525284 original size:29 final size:28
Alignment explanation
Indices: 41525252--41525306 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
41525242 GCTCGAATGC
41525252 TTTCTGTTCTCTT-TTCTCTATTCTTTTTG
1 TTTCTGTTCT-TTATTCTCT-TTCTTTTTG
* *
41525281 TTTCTTTTCTTTATTCTGTTTCTTTT
1 TTTCTGTTCTTTATTCTCTTTCTTTT
41525307 ATTCACTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.04, C:0.18, G:0.05, T:0.73
Consensus pattern (28 bp):
TTTCTGTTCTTTATTCTCTTTCTTTTTG
Found at i:41525289 original size:22 final size:23
Alignment explanation
Indices: 41525251--41525297 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
41525241 TGCTCGAATG
41525251 CTTTCTGTTCTCTTTTCTCTATT
1 CTTTCTGTTCTCTTTTCTCTATT
* *
41525274 CTTTTTGTT-TCTTTTCTTTATT
1 CTTTCTGTTCTCTTTTCTCTATT
41525296 CT
1 CT
41525298 GTTTCTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.04, C:0.21, G:0.04, T:0.70
Consensus pattern (23 bp):
CTTTCTGTTCTCTTTTCTCTATT
Found at i:41525309 original size:14 final size:12
Alignment explanation
Indices: 41525261--41525310 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
41525251 CTTTCTGTTC
*
41525261 TCTTTTCTCTAT
1 TCTTTTCTTTAT
*
41525273 TCTTTT-TGT-T
1 TCTTTTCTTTAT
41525283 TCTTTTCTTTAT
1 TCTTTTCTTTAT
41525295 TCTGTTTCTTTTAT
1 TCT-TTTC-TTTAT
41525309 TC
1 TC
41525311 ACTTTAGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 7 0.22
11 4 0.12
12 10 0.31
13 4 0.12
14 7 0.22
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (12 bp):
TCTTTTCTTTAT
Found at i:41527014 original size:24 final size:24
Alignment explanation
Indices: 41526982--41527029 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
41526972 CATGTTCTCC
41526982 ATCTTATCATTACTTAGAATTTTT
1 ATCTTATCATTACTTAGAATTTTT
41527006 ATCTTATCATTACTTAGAATTTTT
1 ATCTTATCATTACTTAGAATTTTT
41527030 GTCCTATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (24 bp):
ATCTTATCATTACTTAGAATTTTT
Found at i:41528312 original size:19 final size:20
Alignment explanation
Indices: 41528272--41528323 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
41528262 TCAGCATTTA
41528272 AATCAAGTTAAAATGGTTTC
1 AATCAAGTTAAAATGGTTTC
*
41528292 AATCAAGTTAAAAT-TTTTC
1 AATCAAGTTAAAATGGTTTC
41528311 AATCAAAGTTAAA
1 AATC-AAGTTAAA
41528324 TTATTTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 8 0.27
20 22 0.73
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.35
Consensus pattern (20 bp):
AATCAAGTTAAAATGGTTTC
Found at i:41529670 original size:18 final size:19
Alignment explanation
Indices: 41529647--41529690 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
41529637 TCTCACACCA
*
41529647 TTAAATTTAA-TAGAAATT
1 TTAAATTCAATTAGAAATT
* *
41529665 TTAAATTCAATTTGAATTT
1 TTAAATTCAATTAGAAATT
41529684 TTAAATT
1 TTAAATT
41529691 AAAAAATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (19 bp):
TTAAATTCAATTAGAAATT
Found at i:41532451 original size:63 final size:62
Alignment explanation
Indices: 41532326--41532456 Score: 253
Period size: 63 Copynumber: 2.1 Consensus size: 62
41532316 CATGTTCGAA
41532326 TGTTATTGTTTTGAGTAGCATATTTTGTAGTACTAATTATGGAAAAGTCATTATAAACGGAT
1 TGTTATTGTTTTGAGTAGCATATTTTGTAGTACTAATTATGGAAAAGTCATTATAAACGGAT
41532388 TGTTATTGTTTTGAGTAGCATATTTTGTAGTAACTAATTATGGAAAAGTCATTATAAACGGAT
1 TGTTATTGTTTTGAGTAGCATATTTTGTAGT-ACTAATTATGGAAAAGTCATTATAAACGGAT
41532451 TGTTAT
1 TGTTAT
41532457 CTTTGTTTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
62 31 0.46
63 37 0.54
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (62 bp):
TGTTATTGTTTTGAGTAGCATATTTTGTAGTACTAATTATGGAAAAGTCATTATAAACGGAT
Found at i:41536350 original size:19 final size:20
Alignment explanation
Indices: 41536310--41536359 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
41536300 ATTACAAAAT
*
41536310 AATTCAAAATAATTTTTAAA
1 AATTTAAAATAATTTTTAAA
41536330 AATTTAAAATAATTTTT-AA
1 AATTTAAAATAATTTTTAAA
41536349 AATTTAAAATA
1 AATTTAAAATA
41536360 TTTATAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTTAAAATAATTTTTAAA
Found at i:41536367 original size:18 final size:19
Alignment explanation
Indices: 41536310--41536367 Score: 73
Period size: 20 Copynumber: 3.1 Consensus size: 19
41536300 ATTACAAAAT
* *
41536310 AATTCAAAATAATTTTTAAA
1 AATTTAAAATAATTTAT-AA
*
41536330 AATTTAAAATAATTTTTAA
1 AATTTAAAATAATTTATAA
41536349 AATTTAAAAT-ATTTATAA
1 AATTTAAAATAATTTATAA
41536367 A
1 A
41536368 GATTCCAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.22
19 12 0.33
20 16 0.44
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTTAAAATAATTTATAA
Found at i:41548653 original size:35 final size:35
Alignment explanation
Indices: 41548589--41548676 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
41548579 ATATACTCAG
* * * *
41548589 TCAGACACAGATGCAGATTCGGGCTTAAGCCCAT-
1 TCAGATACAGATACAGATTCAGGCCTAAGCCCATC
* *
41548623 TACGGATATAGATACAGATTCAGGCCTAAGCCCATC
1 T-CAGATACAGATACAGATTCAGGCCTAAGCCCATC
41548659 TCAGATACAGATACAGAT
1 TCAGATACAGATACAGAT
41548677 GTACAAATCA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
34 1 0.02
35 42 0.95
36 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (35 bp):
TCAGATACAGATACAGATTCAGGCCTAAGCCCATC
Found at i:41550270 original size:19 final size:19
Alignment explanation
Indices: 41550246--41550282 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41550236 ACAATGCCCG
41550246 ATAAATGATAATACCTGAA
1 ATAAATGATAATACCTGAA
*
41550265 ATAAATGATAATGCCTGA
1 ATAAATGATAATACCTGA
41550283 TAAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.27
Consensus pattern (19 bp):
ATAAATGATAATACCTGAA
Found at i:41550287 original size:17 final size:17
Alignment explanation
Indices: 41550238--41550292 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
41550228 CATATTCGAC
*
41550238 AATGCCCGATAAATGAT
1 AATGCCTGATAAATGAT
*
41550255 AATACCTGAAATAAATGAT
1 AATGCCTG--ATAAATGAT
*
41550274 AATGCCTGATAAATAAT
1 AATGCCTGATAAATGAT
41550291 AA
1 AA
41550293 ATGATAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 16 0.50
19 16 0.50
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (17 bp):
AATGCCTGATAAATGAT
Found at i:41558587 original size:22 final size:22
Alignment explanation
Indices: 41558551--41558599 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
41558541 TAATCGTAGA
41558551 TTTATTATTCTATTTTAATTAT
1 TTTATTATTCTATTTTAATTAT
41558573 TTTAGTTATTC-ATTTTAATTAT
1 TTTA-TTATTCTATTTTAATTAT
41558595 TTTAT
1 TTTAT
41558600 CTGATTTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.04
22 19 0.73
23 6 0.23
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTATTATTCTATTTTAATTAT
Found at i:41561649 original size:22 final size:21
Alignment explanation
Indices: 41561615--41561655 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
41561605 GTTGAAATGT
41561615 CACACAGGCGTGTTGCCCCTCC
1 CACACAGGCGTG-TGCCCCTCC
* *
41561637 CACACGGGTGTGTGCCCCT
1 CACACAGGCGTGTGCCCCT
41561656 ATGTTAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.12, C:0.41, G:0.27, T:0.20
Consensus pattern (21 bp):
CACACAGGCGTGTGCCCCTCC
Found at i:41563220 original size:19 final size:19
Alignment explanation
Indices: 41563196--41563233 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
41563186 AGATAAAATA
41563196 ATCAAAAAATTAAAGCTAT
1 ATCAAAAAATTAAAGCTAT
41563215 ATCAAAAAATTAAAGCTAT
1 ATCAAAAAATTAAAGCTAT
41563234 CATCTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.26
Consensus pattern (19 bp):
ATCAAAAAATTAAAGCTAT
Found at i:41565441 original size:38 final size:39
Alignment explanation
Indices: 41565359--41565540 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
41565349 AATGTTCGAG
41565359 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
41565398 TGATATCCGGGCTAAGCCCGAAGGCAATTG-GCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
41565436 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* ** *
41565475 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
41565515 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
41565541 GTTTGAACGA
Statistics
Matches: 126, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
38 38 0.30
39 50 0.40
40 38 0.30
ACGTcount: A:0.24, C:0.23, G:0.30, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:41573377 original size:39 final size:39
Alignment explanation
Indices: 41573330--41573512 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
41573320 AATGTTCGAG
41573330 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
41573369 TGATATCCGGGCTAAGCCCGAAGGCAATTGGGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
41573408 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* ** *
41573447 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
41573487 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
41573513 GTTTGAACGA
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 88 0.70
40 38 0.30
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:41586721 original size:60 final size:60
Alignment explanation
Indices: 41586583--41586721 Score: 138
Period size: 60 Copynumber: 2.3 Consensus size: 60
41586573 TTTGCACAAT
* ** * *
41586583 TGTGCCCCTGTTCGCACTTTGGTGCCCCTGTATACACTCCAGTGTCTCTATTTGCATGCC
1 TGTGCCCCTGTTTGCACTTCAGTGCCCCTATATACACTCCAGTGTCTCTATTTGCATGCA
* *** * * *
41586643 TGTGCTCCTGTTCT-CACTTCAGTGCCCCTATATACACTTTGGTGT-TCTTGTTTGTATGTA
1 TGTGCCCCTGTT-TGCACTTCAGTGCCCCTATATACACTCCAGTGTCTC-TATTTGCATGCA
41586703 TGTGCCCCTGTTTGCACTT
1 TGTGCCCCTGTTTGCACTT
41586722 GGGTGCTCTT
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
59 3 0.05
60 60 0.95
ACGTcount: A:0.12, C:0.29, G:0.19, T:0.40
Consensus pattern (60 bp):
TGTGCCCCTGTTTGCACTTCAGTGCCCCTATATACACTCCAGTGTCTCTATTTGCATGCA
Found at i:41588975 original size:37 final size:37
Alignment explanation
Indices: 41588924--41588997 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
41588914 TAATCACTAA
41588924 GCCTCAAACATAGGGTACGATGCCAATGCCATGTTCC
1 GCCTCAAACATAGGGTACGATGCCAATGCCATGTTCC
* *
41588961 GCCTCAAACGTAGGGTACGATGCCGATGCCATGTTCC
1 GCCTCAAACATAGGGTACGATGCCAATGCCATGTTCC
41588998 AAACATGGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (37 bp):
GCCTCAAACATAGGGTACGATGCCAATGCCATGTTCC
Found at i:41589095 original size:49 final size:49
Alignment explanation
Indices: 41588978--41589343 Score: 219
Period size: 49 Copynumber: 7.7 Consensus size: 49
41588968 ACGTAGGGTA
* * * *
41588978 CGATGCCGATGCCATGTTCCAAACATGGTCTTACACT-A-GCTCACATAT
1 CGATGCCAATGCCATGTCCCAAACA-GGTCTTACACTGACTCTCATATAT
* * * * * *
41589026 CTAAGTCGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATAT
1 CGATGCCAATGCCATGTCCCAAACAGGTCTTACACTGACTCTCATATAT
* * *
41589075 CGATGCCAATGCCATATCCCAAACAGGTCTTACACTGGCTCTCATCTAT
1 CGATGCCAATGCCATGTCCCAAACAGGTCTTACACTGACTCTCATATAT
* * * * *
41589124 CGGTGTCGATGCCATGTCCCAAACAGGTCTTACACTGA----CACATGT
1 CGATGCCAATGCCATGTCCCAAACAGGTCTTACACTGACTCTCATATAT
* ** * *
41589169 C-AAGCTGATGCCATGTCCCAGACAGGTCTTACACT-AGCT-TGCATATCT
1 CGATGCCAATGCCATGTCCCAAACAGGTCTTACACTGA-CTCT-CATATAT
* * * * * * * *
41589217 CGAGGCCGATG-CATCTCCCAAACA-TTACTTATACTGGCTCTC--GTCT
1 CGATGCCAATGCCATGTCCCAAACAGGT-CTTACACTGACTCTCATATAT
* * * * *
41589263 CAATGCCGATG-CATGTCCCAGACATGTCTTACACTGGCTCTCATA-AT
1 CGATGCCAATGCCATGTCCCAAACAGGTCTTACACTGACTCTCATATAT
* *
41589310 -G-TGGCCGATG-CATGTCCCAAACATGTCTTACACT
1 CGAT-GCCAATGCCATGTCCCAAACAGGTCTTACACT
41589344 AGCACACGTA
Statistics
Matches: 253, Mismatches: 50, Indels: 32
0.76 0.15 0.10
Matches are distributed among these distances:
43 1 0.00
44 29 0.11
45 6 0.02
46 67 0.26
47 14 0.06
48 48 0.19
49 88 0.35
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (49 bp):
CGATGCCAATGCCATGTCCCAAACAGGTCTTACACTGACTCTCATATAT
Found at i:41589150 original size:98 final size:97
Alignment explanation
Indices: 41588978--41589162 Score: 264
Period size: 98 Copynumber: 1.9 Consensus size: 97
41588968 ACGTAGGGTA
* * * *
41588978 CGATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATCTAAGTCGATGCCATGT
1 CGATGCCAATGCCATATCCCAAACATGGTCTTACACTAGCTCACATATCGAAGTCGATGCCATGT
*
41589043 CCCAGACAGGTCTTACACTGACTTTCATATAT
66 CCCAAACAGGTCTTACACTGACTTTCATATAT
* * **
41589075 CGATGCCAATGCCATATCCCAAACA-GGTCTTACACTGGCTCTCATCTATCGGTGTCGATGCCAT
1 CGATGCCAATGCCATATCCCAAACATGGTCTTACACTAGCTCACA--TATCGAAGTCGATGCCAT
41589139 GTCCCAAACAGGTCTTACACTGAC
64 GTCCCAAACAGGTCTTACACTGAC
41589163 ACATGTCAAG
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
96 17 0.22
97 22 0.29
98 38 0.49
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (97 bp):
CGATGCCAATGCCATATCCCAAACATGGTCTTACACTAGCTCACATATCGAAGTCGATGCCATGT
CCCAAACAGGTCTTACACTGACTTTCATATAT
Found at i:41593213 original size:14 final size:14
Alignment explanation
Indices: 41593179--41593205 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41593169 CCCACATAAT
41593179 ATTTTTTATTTTTC
1 ATTTTTTATTTTTC
41593193 ATTTTTTATTTTT
1 ATTTTTTATTTTT
41593206 TTCTTTTTTC
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:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (14 bp):
ATTTTTTATTTTTC
Found at i:41603518 original size:24 final size:24
Alignment explanation
Indices: 41603482--41603528 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
41603472 ATAGCCTGAT
*
41603482 TAGTAGTGATATATGATCTTTGAA
1 TAGTAGTGATATATGATCCTTGAA
*
41603506 TAGTAGTGCTATATGATCCTTGA
1 TAGTAGTGATATATGATCCTTGA
41603529 CTATATAGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (24 bp):
TAGTAGTGATATATGATCCTTGAA
Found at i:41604969 original size:30 final size:32
Alignment explanation
Indices: 41604908--41604972 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
41604898 TGAATCTGTC
* *
41604908 AATACTATTAACAGTGTTATCAGTCAGCAGTT
1 AATACTATTAACACTGTTAACAGTCAGCAGTT
*
41604940 AATACTATTAACACTG-TAACGGT-AGCAGTT
1 AATACTATTAACACTGTTAACAGTCAGCAGTT
41604970 AAT
1 AAT
41604973 GTTATTAGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 10 0.33
31 5 0.17
32 15 0.50
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (32 bp):
AATACTATTAACACTGTTAACAGTCAGCAGTT
Found at i:41607121 original size:3 final size:3
Alignment explanation
Indices: 41607113--41607138 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41607103 GCAAGAGGTG
41607113 GTT GTT GTT GTT GTT GTT GTT GTT GT
1 GTT GTT GTT GTT GTT GTT GTT GTT GT
41607139 AAATACATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (3 bp):
GTT
Found at i:41610533 original size:38 final size:39
Alignment explanation
Indices: 41610490--41610575 Score: 120
Period size: 40 Copynumber: 2.2 Consensus size: 39
41610480 AACCAGTCCA
* *
41610490 ACACACCA-TGTGGGGATAGAATCGACCCACCCAACCCT
1 ACACACCAGTATGGGGATAGAATCAACCCACCCAACCCT
* *
41610528 ACACACCAAGTATGGGGATATAATCAACCCATCCAACCCT
1 ACACACC-AGTATGGGGATAGAATCAACCCACCCAACCCT
41610568 ACACACCA
1 ACACACCA
41610576 AAAGGTACTG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 7 0.17
39 2 0.05
40 33 0.79
ACGTcount: A:0.36, C:0.36, G:0.14, T:0.14
Consensus pattern (39 bp):
ACACACCAGTATGGGGATAGAATCAACCCACCCAACCCT
Found at i:41610547 original size:40 final size:40
Alignment explanation
Indices: 41610500--41610576 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
41610490 ACACACCATG
*
41610500 TGGGGATAGAATCGACCCACCCAACCCTACACACCAAGTA
1 TGGGGATAGAATCAACCCACCCAACCCTACACACCAAGTA
* *
41610540 TGGGGATATAATCAACCCATCCAACCCTACACACCAA
1 TGGGGATAGAATCAACCCACCCAACCCTACACACCAA
41610577 AAGGTACTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.36, C:0.35, G:0.14, T:0.14
Consensus pattern (40 bp):
TGGGGATAGAATCAACCCACCCAACCCTACACACCAAGTA
Found at i:41617641 original size:38 final size:39
Alignment explanation
Indices: 41617599--41617684 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 39
41617589 GACCAGCCCA
* * *
41617599 ACACACCA-TGTGGGGATAGAATCGACCCACCCA-ACCCT
1 ACACACCAGTATGGAGATAGAATCAACCCACCCACA-CCT
* *
41617637 ACACACCAAGTATGGAGATATAATCAACCCATCCACACCT
1 ACACACC-AGTATGGAGATAGAATCAACCCACCCACACCT
41617677 ACACACCA
1 ACACACCA
41617685 AAAGGTACCG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
38 7 0.17
39 2 0.05
40 30 0.75
41 1 0.03
ACGTcount: A:0.37, C:0.36, G:0.13, T:0.14
Consensus pattern (39 bp):
ACACACCAGTATGGAGATAGAATCAACCCACCCACACCT
Found at i:41619434 original size:140 final size:140
Alignment explanation
Indices: 41619177--41619658 Score: 709
Period size: 140 Copynumber: 3.5 Consensus size: 140
41619167 GTTACAAAAT
* * * * *
41619177 AATTAAAAAATCTTGAAGCAACATGAAACGAAAAATACAAATGTGAGTAGTAGAGGAATCCAACT
1 AATTTAAAAAGCTTGAAGCAACATGAAACAAAAAATACAAATGTGAGTAGGAGAGGAATCAAACT
* *
41619242 CGAGACTCAAGGATGTAATTACAACTATGTAATCACCTAACGAAAAAACTAATATGTTAAAAAAC
66 CGAGACTCAAGGATGTAATTACAACTATCTAATCATCTAACGAAAAAACTAATATGTTAAAAAAC
41619307 ATTAATTAAA
131 ATTAATTAAA
* * *
41619317 AATTTAAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATTTGAGTAGGAGAGAAATCAAACT
1 AATTTAAAAAGCTTGAAGCAACATGAAACAAAAAATACAAATGTGAGTAGGAGAGGAATCAAACT
* ** * *
41619382 CGAGACTCAAAGATGTAACAACAACTATCTAATCATCTAACCAAAGAACTAATATGTTAAAAAA-
66 CGAGACTCAAGGATGTAATTACAACTATCTAATCATCTAACGAAAAAACTAATATGTTAAAAAAC
41619446 ATTAATT-AA
131 ATTAATTAAA
* * * *
41619455 AATTTAAAAAGCTTGAAGCAACATGAAACAAAAAATACAAATGTGAGTAGTAGATGAATCCAGCT
1 AATTTAAAAAGCTTGAAGCAACATGAAACAAAAAATACAAATGTGAGTAGGAGAGGAATCAAACT
* *
41619520 TGAGACTCAAGGATGTAATTACAACTATCTAA-CAATGTAACGAAAAAACTAATATGTTAAAAAA
66 CGAGACTCAAGGATGTAATTACAACTATCTAATC-ATCTAACGAAAAAACTAATATGTTAAAAAA
41619584 CATTAATTAAA
130 CATTAATTAAA
* * * *
41619595 AAATTAAAAAGCTTAAAGCAACATGAAATAAAAAATACAAATGTGAGTGGGAGAGGAATCAAAC
1 AATTTAAAAAGCTTGAAGCAACATGAAACAAAAAATACAAATGTGAGTAGGAGAGGAATCAAAC
41619659 CTAAAACTCA
Statistics
Matches: 302, Mismatches: 37, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
137 1 0.00
138 115 0.38
139 14 0.05
140 172 0.57
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.23
Consensus pattern (140 bp):
AATTTAAAAAGCTTGAAGCAACATGAAACAAAAAATACAAATGTGAGTAGGAGAGGAATCAAACT
CGAGACTCAAGGATGTAATTACAACTATCTAATCATCTAACGAAAAAACTAATATGTTAAAAAAC
ATTAATTAAA
Found at i:41628430 original size:39 final size:39
Alignment explanation
Indices: 41628376--41628537 Score: 166
Period size: 39 Copynumber: 4.2 Consensus size: 39
41628366 ATGATACCCG
* *
41628376 GGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCC
1 GGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATCC
* * *
41628415 GGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATATCG
1 GGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATATCC
* * ** *
41628454 GGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCC
1 GGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATCC
* * * *
41628493 GGGTTAAGACCC-AAGGCAATTGTGCTTGTGGTTATATCC
1 -GGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATCC
41628532 GGCTAA
1 GGCTAA
41628538 ATTCCGAAGA
Statistics
Matches: 98, Mismatches: 22, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
38 6 0.06
39 80 0.82
40 12 0.12
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
GGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATCC
Found at i:41628509 original size:78 final size:78
Alignment explanation
Indices: 41628374--41628537 Score: 188
Period size: 78 Copynumber: 2.1 Consensus size: 78
41628364 GAATGATACC
* * ** *
41628374 CGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCGGCTAAGACCCGAAGGC-ATTCGT
1 CGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGCTAAGACCCGAAGGCAATT-GT
*
41628438 GCGAGTTGTTATAT
65 GCGAGTGGTTATAT
* * *
41628452 CGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCGGGTTAAGACCC-AAGGCAATTGT
1 CGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCC-GGCTAAGACCCGAAGGCAATTGT
**
41628516 GCTTGTGGTTATAT
65 GCGAGTGGTTATAT
*
41628530 CCGGCTAA
1 CGGGCTAA
41628538 ATTCCGAAGA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
78 59 0.82
79 13 0.18
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (78 bp):
CGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGCTAAGACCCGAAGGCAATTGTG
CGAGTGGTTATAT
Found at i:41635170 original size:13 final size:13
Alignment explanation
Indices: 41635154--41635178 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41635144 CAAAACTAGG
41635154 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
41635167 AAGAAAAAGAAA
1 AAGAAAAAGAAA
41635179 GCTTCATCCT
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:41644958 original size:3 final size:3
Alignment explanation
Indices: 41644950--41644983 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
41644940 AATGACAATG
41644950 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
41644984 ACGTAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:41645611 original size:25 final size:25
Alignment explanation
Indices: 41645566--41645619 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
41645556 ATGATACAAT
*
41645566 ATAATAATAATGTAAAGAAAATAAA
1 ATAATAATAATGTAAAGAAAAGAAA
* *
41645591 ATAATAAT-ATTTATAATAAAAGAAA
1 ATAATAATAATGTA-AAGAAAAGAAA
41645616 ATAA
1 ATAA
41645620 AAGAGTGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (25 bp):
ATAATAATAATGTAAAGAAAAGAAA
Found at i:41645808 original size:13 final size:13
Alignment explanation
Indices: 41645790--41645816 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41645780 AAATGCGCGT
41645790 GAAACAACAGAGG
1 GAAACAACAGAGG
41645803 GAAACAACAGAGG
1 GAAACAACAGAGG
41645816 G
1 G
41645817 CTAAAGTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.15, G:0.33, T:0.00
Consensus pattern (13 bp):
GAAACAACAGAGG
Found at i:41646249 original size:13 final size:13
Alignment explanation
Indices: 41646233--41646257 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41646223 CATCCGCCGC
41646233 CGCCGGCCACCGT
1 CGCCGGCCACCGT
41646246 CGCCGGCCACCG
1 CGCCGGCCACCG
41646258 AGCATGGTGG
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:0.08, C:0.56, G:0.32, T:0.04
Consensus pattern (13 bp):
CGCCGGCCACCGT
Found at i:41647411 original size:10 final size:10
Alignment explanation
Indices: 41647383--41647413 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
41647373 TCTTCCATTA
*
41647383 TGAAGATAAT
1 TGAAGATATT
41647393 TGAAGATATT
1 TGAAGATATT
41647403 TGAAGATATT
1 TGAAGATATT
41647413 T
1 T
41647414 TTATATACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (10 bp):
TGAAGATATT
Found at i:41648003 original size:16 final size:15
Alignment explanation
Indices: 41647977--41648024 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
41647967 TAGGGAAACA
*
41647977 ACTGTTATTTAGAAT
1 ACTGTTGTTTAGAAT
* *
41647992 AGTTGTTGTTTAGAAC
1 A-CTGTTGTTTAGAAT
41648008 ACTGTTGTTTGAGAAT
1 ACTGTTGTTT-AGAAT
41648024 A
1 A
41648025 TTTATATCCA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 9 0.35
16 17 0.65
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (15 bp):
ACTGTTGTTTAGAAT
Found at i:41653355 original size:40 final size:40
Alignment explanation
Indices: 41653158--41653341 Score: 239
Period size: 40 Copynumber: 4.6 Consensus size: 40
41653148 GAATGATGTT
* * *
41653158 CGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAAC
* * *
41653198 CAGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAAAC
1 CGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAAC
41653238 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-C
*
41653278 CGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAAC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAC
* *
41653318 CGGGCTATGTCCTGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTG
41653342 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
39 3 0.02
40 114 0.90
41 10 0.08
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAC
Found at i:41656214 original size:39 final size:40
Alignment explanation
Indices: 41656093--41656284 Score: 176
Period size: 40 Copynumber: 4.8 Consensus size: 40
41656083 GGATATAACG
* * ** *
41656093 ACTCGCTCAAATGCCTTCAGGACAAAGCCCAG-TTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* * * *
41656133 ACTTGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
*
41656173 ACTCGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * * * *
41656212 ACTCGCACGAACGCCTTC-GGATCTTAGTCCGGATATAGTC
1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTA
**
41656252 ACTTAACACAAA-GCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
41656285 CATCATTCAA
Statistics
Matches: 124, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 80 0.65
41 11 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:41661167 original size:39 final size:39
Alignment explanation
Indices: 41661120--41661302 Score: 231
Period size: 39 Copynumber: 4.6 Consensus size: 39
41661110 AATGTTCGAG
41661120 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
41661159 TGATATCCGGGCTAAGCCCGAAGGCAATTGGGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * * *
41661198 TGATATCCAGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* ** *
41661237 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
41661277 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
41661303 GTTTGAACGA
Statistics
Matches: 124, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 86 0.69
40 38 0.31
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:41663090 original size:30 final size:30
Alignment explanation
Indices: 41663054--41663112 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
41663044 TGGGGCAAGC
**
41663054 CGTGTGTCACACATGGCCAAGACACATGCT
1 CGTGTGTCACACACAGCCAAGACACATGCT
* *
41663084 CGTGTGTCACATACAGCCTAGACACATGC
1 CGTGTGTCACACACAGCCAAGACACATGC
41663113 CTGTGTATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (30 bp):
CGTGTGTCACACACAGCCAAGACACATGCT
Found at i:41663982 original size:42 final size:42
Alignment explanation
Indices: 41663918--41664029 Score: 147
Period size: 42 Copynumber: 2.7 Consensus size: 42
41663908 TACCATACCA
* * *
41663918 ATGCCATATCCCAGATATGGTCTTACATG-GGATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAG-TCTCATATAG
* *
41663960 ATGCTATATCCTAGATATGGTCTTACACGAAGTCTCATATAG
1 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATAG
41664002 ATGCCATATCCCAGATATGG-CTTTACAC
1 ATGCCATATCCCAGATATGGTC-TTACAC
41664030 ATAGTCTTAG
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
41 1 0.02
42 59 0.97
43 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATAG
Found at i:41684700 original size:29 final size:29
Alignment explanation
Indices: 41684668--41684803 Score: 148
Period size: 29 Copynumber: 4.7 Consensus size: 29
41684658 ATACCCTTCG
** * *
41684668 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
* * * *
41684697 AGCTTGCACACATAGTGTCATATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
* *
41684726 AGCAT-GCATACTTAGTGCCTTATATTTCC
1 AGC-TCGCACACTTAGTGCCATATATTTCC
*
41684755 AGCACGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
41684784 AGCACGCACACTTAGTGCCA
1 AGCTCGCACACTTAGTGCCA
41684804 ATCTCGTCAC
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
29 91 0.99
30 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.30
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCATATATTTCC
Found at i:41684743 original size:58 final size:58
Alignment explanation
Indices: 41684643--41684802 Score: 167
Period size: 58 Copynumber: 2.8 Consensus size: 58
41684633 AATTTAAGCC
* *** * * ** * *
41684643 CGCACACACAGTGCCATACCCTTCGAGCTCGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCCGTATATTTCCAGCA
* * * * * *
41684701 TGCACACATAGTGTCATATTTTTCCAGCATGCATACTTAGTGCCTTATATTTCCAGCA
1 CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCCGTATATTTCCAGCA
*
41684759 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCC
1 CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCC
41684803 AATCTCGTCA
Statistics
Matches: 81, Mismatches: 21, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
58 81 1.00
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.28
Consensus pattern (58 bp):
CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCCGTATATTTCCAGCA
Found at i:41685656 original size:142 final size:141
Alignment explanation
Indices: 41685447--41685740 Score: 554
Period size: 142 Copynumber: 2.1 Consensus size: 141
41685437 AAATTCTATA
41685447 GCATGGCCGAATACTCATGCACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
1 GCATGGCCGAATACTCATGCACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
41685512 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
66 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
*
41685577 GAAGACAACAT
131 GAAAACAACAT
41685588 GCATGGCCGAATACTCATGCACACACACACATAACAACAA-AACTCAATGGCACAAAATTTCCTT
1 GCATGGCCGAATACTCATG--CACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTT
41685652 TTTGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCA
64 TTTGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCA
41685717 AGGAAAACAACAT
129 AGGAAAACAACAT
41685730 GCATGGCCGAA
1 GCATGGCCGAA
41685741 ATTTAACTCA
Statistics
Matches: 150, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
141 19 0.13
142 112 0.75
143 19 0.13
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.21
Consensus pattern (141 bp):
GCATGGCCGAATACTCATGCACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
GAAAACAACAT
Found at i:41699019 original size:24 final size:23
Alignment explanation
Indices: 41698992--41699051 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 23
41698982 GGGTGTTACA
41698992 ATTGGATTCAAATTTTAATACTAG
1 ATTGGATTCAAATTTTAATA-TAG
*
41699016 ATTGGA-TC-AA-TTTCATATAG
1 ATTGGATTCAAATTTTAATATAG
*
41699036 ATT-GATACAAATTTTA
1 ATTGGATTCAAATTTTA
41699052 TGTTATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
19 2 0.07
20 7 0.23
21 8 0.27
22 5 0.17
23 2 0.07
24 6 0.20
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (23 bp):
ATTGGATTCAAATTTTAATATAG
Found at i:41699164 original size:14 final size:15
Alignment explanation
Indices: 41699145--41699177 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
41699135 CTACCAAATT
41699145 AAATAAATGTTT-TA
1 AAATAAATGTTTCTA
*
41699159 AAATAATTGTTTCTA
1 AAATAAATGTTTCTA
41699174 AAAT
1 AAAT
41699178 TTCATTAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (15 bp):
AAATAAATGTTTCTA
Found at i:41699300 original size:2 final size:2
Alignment explanation
Indices: 41699293--41699318 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41699283 CGCATCATGA
41699293 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
41699319 GTAAATGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41701354 original size:2 final size:2
Alignment explanation
Indices: 41701347--41701376 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41701337 TAAACTACAA
41701347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41701377 GTGTGTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41703728 original size:40 final size:40
Alignment explanation
Indices: 41703622--41703805 Score: 147
Period size: 40 Copynumber: 4.6 Consensus size: 40
41703612 TGCTGGAAAT
* * * * * **
41703622 TATAACCGGGTTAAGACCCGAAGGCAATGGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
*
41703662 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAT
1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
* * * *
41703702 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-AATC-G
1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
* * * * * * *
41703740 TGATATCCGGGTTAAGTCCCGTAGGCCTTGGTGCGGGTTAC
1 T-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
* * *
41703781 CATATCCGGGCTATGTCCCGAAGGC
1 TATATCCGGGCTAAGACCCGAAGGC
41703806 GTTTGAACGA
Statistics
Matches: 115, Mismatches: 26, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
38 1 0.01
39 29 0.25
40 85 0.74
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.23
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
Found at i:41711837 original size:40 final size:40
Alignment explanation
Indices: 41711731--41711914 Score: 147
Period size: 40 Copynumber: 4.6 Consensus size: 40
41711721 TGCTGGAAAT
* * * * * **
41711731 TATAACCGGGTTAAGACCCGAAGGCAATGGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
*
41711771 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAT
1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
* * * *
41711811 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-AATC-G
1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
* * * * * * *
41711849 TGATATCCGGGTTAAGTCCCGTAGGCCTTGGTGCGGGTTAC
1 T-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
* * *
41711890 CATATCCGGGCTATGTCCCGAAGGC
1 TATATCCGGGCTAAGACCCGAAGGC
41711915 GTTTGAACGA
Statistics
Matches: 115, Mismatches: 26, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
38 1 0.01
39 29 0.25
40 85 0.74
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.23
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
Found at i:41718856 original size:40 final size:39
Alignment explanation
Indices: 41718785--41718869 Score: 116
Period size: 40 Copynumber: 2.2 Consensus size: 39
41718775 TAACGACTTA
* **
41718785 TCGGCTAAAATGGGACTTAGTGTGCGGTTTGAAATAGCT
1 TCGGCTAAAATGGCACTTAGTGTGCAATTTGAAATAGCT
* *
41718824 TCGGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGCT
1 TCGGCTAAAA-TGGCACTTAGTGTGCAATTTGAAATAGCT
41718864 TCGGCT
1 TCGGCT
41718870 GTATATAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 10 0.25
40 30 0.75
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.31
Consensus pattern (39 bp):
TCGGCTAAAATGGCACTTAGTGTGCAATTTGAAATAGCT
Found at i:41721681 original size:93 final size:94
Alignment explanation
Indices: 41721547--41721724 Score: 225
Period size: 97 Copynumber: 1.9 Consensus size: 94
41721537 AAATACATGT
* * *
41721547 GAGCGAGTGTAAAACCATGTTTGGAACATGGCATTAGCTTGATAT-GTGTTAGTGTAAGACCATG
1 GAGCCAGTGTAAAACCATGTTTGGAACATGGCATCAGCTTGATATAGAGTTAGTGTAAGACCATG
*
41721611 TCTGGGACATGGTATCGGCACGGAAAGGA
66 TCTGGGACATGGCATCGGCACGGAAAGGA
* * * *
41721640 GAGCCAGTGTAAGACCATG-TTGGGATATGGCATCGGCCTTGATATAAGAGAGTTAGTGTAAGAC
1 GAGCCAGTGTAAAACCATGTTTGGAACATGGCATCAG-CTTGATAT---AGAGTTAGTGTAAGAC
*
41721704 CATGTTTGGGACATGGCATCG
62 CATGTCTGGGACATGGCATCG
41721725 ACTCGATATG
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
92 13 0.18
93 25 0.35
97 33 0.46
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (94 bp):
GAGCCAGTGTAAAACCATGTTTGGAACATGGCATCAGCTTGATATAGAGTTAGTGTAAGACCATG
TCTGGGACATGGCATCGGCACGGAAAGGA
Found at i:41721703 original size:49 final size:47
Alignment explanation
Indices: 41721594--41721724 Score: 156
Period size: 49 Copynumber: 2.7 Consensus size: 47
41721584 CTTGATATGT
* *
41721594 GTTAGTGTAAGACCATGTCTGGGACATGGTATCGGCACGGAAAGGAGA
1 GTTAGTGTAAGACCATGT-TGGGACATGGCATCGGCACGGAAAAGAGA
** * *
41721642 GCCAGTGTAAGACCATGTTGGGATATGGCATCGGC-CTTGATATAAGAGA
1 GTTAGTGTAAGACCATGTTGGGACATGGCATCGGCAC-GGA-A-AAGAGA
41721691 GTTAGTGTAAGACCATGTTTGGGACATGGCATCG
1 GTTAGTGTAAGACCATG-TTGGGACATGGCATCG
41721725 ACTCGATATG
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
46 1 0.01
47 17 0.24
48 17 0.24
49 20 0.29
50 15 0.21
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.24
Consensus pattern (47 bp):
GTTAGTGTAAGACCATGTTGGGACATGGCATCGGCACGGAAAAGAGA
Found at i:41721761 original size:97 final size:95
Alignment explanation
Indices: 41721594--41721855 Score: 226
Period size: 97 Copynumber: 2.8 Consensus size: 95
41721584 CTTGATATGT
* * * * * *
41721594 GTTAGTGTAAGACCATGTCTGGGACATGGTATCGGCACGGA-AAG-GAGAGCCAGTGTAAGACCA
1 GTTAGTGTAAGACCATGTCTGGGACATGGCATCGACTC-GATATGTGATA-ACA-TGTAAGACCA
*
41721657 TGT-TGGGATATGGCATCGGCCTTGATATAAGAGA
63 TGTCTGGGATATGGCATCGGCATTG-TAT-AGAGA
* *
41721691 GTTAGTGTAAGACCATGTTTGGGACATGGCATCGACTCGATATGTGATTACATGTAAGACCATGT
1 GTTAGTGTAAGACCATGTCTGGGACATGGCATCGACTCGATATGTGATAACATGTAAGACCATGT
* *
41721756 CTGGG--A---CATTGGCATTGTATAGTGA
66 CTGGGATATGGCATCGGCATTGTATAGAGA
* * * * *
41721781 TTTCGTGTAAGACCCTGTGTGGGACAGTGGCATCGA-T---T-TGTGATAACATGTAAGACCATA
1 GTTAGTGTAAGACCATGTCTGGGACA-TGGCATCGACTCGATATGTGATAACATGTAAGACCATG
*
41721841 TCTAGGATATGGCAT
65 TCTGGGATATGGCAT
41721856 TGTATGAGCC
Statistics
Matches: 138, Mismatches: 18, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
86 25 0.18
87 1 0.01
88 1 0.01
90 27 0.20
91 15 0.11
92 9 0.07
95 1 0.01
96 15 0.11
97 42 0.30
98 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.28
Consensus pattern (95 bp):
GTTAGTGTAAGACCATGTCTGGGACATGGCATCGACTCGATATGTGATAACATGTAAGACCATGT
CTGGGATATGGCATCGGCATTGTATAGAGA
Found at i:41721824 original size:43 final size:43
Alignment explanation
Indices: 41721695--41721855 Score: 146
Period size: 43 Copynumber: 3.7 Consensus size: 43
41721685 AAGAGAGTTA
*
41721695 GTGTAAGACCATGTTTGGGACATGGCATCGACTCGATATGTGATTAC
1 GTGTAAGACCATGTCTGGGACATGGCATCGA-T--AT-TGTGATTAC
* * * *
41721742 ATGTAAGACCATGTCTGGGACATTGGCATTG-TATAGTGATTTC
1 GTGTAAGACCATGTCTGGGACA-TGGCATCGATATTGTGATTAC
* * *
41721785 GTGTAAGACCCTGTGTGGGACAGTGGCATCGAT-TTGTGATAAC
1 GTGTAAGACCATGTCTGGGACA-TGGCATCGATATTGTGATTAC
* * * *
41721828 ATGTAAGACCATATCTAGGATATGGCAT
1 GTGTAAGACCATGTCTGGGACATGGCAT
41721856 TGTATGAGCC
Statistics
Matches: 93, Mismatches: 19, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
42 6 0.06
43 56 0.60
44 3 0.03
46 1 0.01
47 20 0.22
48 7 0.08
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGATATTGTGATTAC
Found at i:41721830 original size:86 final size:87
Alignment explanation
Indices: 41721695--41721860 Score: 221
Period size: 86 Copynumber: 1.9 Consensus size: 87
41721685 AAGAGAGTTA
* * * *
41721695 GTGTAAGACCATGTTTGGGACATGGCATCGACTCGATATGTGATTACATGTAAGACCATGTCTGG
1 GTGTAAGACCATGTGTGGGACATGGCATCGACT--ATATGTGATAACATGTAAGACCATATCTAG
41721760 GACATTGGCATTGTATAGTGATTTC
64 GACA-TGGCATTGTATAGTGATTTC
*
41721785 GTGTAAGACCCTGTGTGGGACAGTGGCATCGA-T-T-TGTGATAACATGTAAGACCATATCTAGG
1 GTGTAAGACCATGTGTGGGACA-TGGCATCGACTATATGTGATAACATGTAAGACCATATCTAGG
*
41721847 ATATGGCATTGTAT
65 ACATGGCATTGTAT
41721861 GAGCCATATG
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
85 11 0.16
86 27 0.39
87 1 0.01
90 21 0.30
91 9 0.13
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (87 bp):
GTGTAAGACCATGTGTGGGACATGGCATCGACTATATGTGATAACATGTAAGACCATATCTAGGA
CATGGCATTGTATAGTGATTTC
Found at i:41725814 original size:40 final size:39
Alignment explanation
Indices: 41725755--41725839 Score: 125
Period size: 40 Copynumber: 2.2 Consensus size: 39
41725745 TAACAACTTA
**
41725755 TCGGCTAAAATGGCACTTAGTGTGCTGTTCGAAATAGCT
1 TCGGCTAAAATGGCACTTAGTGTGCAATTCGAAATAGCT
* *
41725794 TCGGCTAAAAGTGGCACTTAGTGTGCAATTTGAGATAGCT
1 TCGGCTAAAA-TGGCACTTAGTGTGCAATTCGAAATAGCT
41725834 TCGGCT
1 TCGGCT
41725840 GTATATTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 10 0.24
40 31 0.76
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.31
Consensus pattern (39 bp):
TCGGCTAAAATGGCACTTAGTGTGCAATTCGAAATAGCT
Found at i:41732134 original size:79 final size:79
Alignment explanation
Indices: 41732001--41732218 Score: 205
Period size: 79 Copynumber: 2.7 Consensus size: 79
41731991 GAATCACGTA
* * * * * *
41732001 CCTTCGGAAT-TTAA-CCGGATATAGCT-ACTCGCTCAAATGCCTTCTGGACATAGCCCGG-TTA
1 CCTTCGG-ATCTTAACCCAGATATAG-TAACTCGCACCAATGCCTTC-GGGCTTAGCCCGGAAT-
41732062 TAGTAACTCGCACAAATG
62 TAGTAACTCGCACAAATG
* *
41732080 CCTTCGGGA-CTTAACCCAGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCAGAATTAG
1 CCTTC-GGATCTTAACCCAGATATAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGGAATTAG
41732144 TAACTCGCACAAATG
65 TAACTCGCACAAATG
** * * * *
41732159 CCTTCGGATCTTAGTCCGGATATAGTCACTTAGCA-CAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGATCTTAACCCAGATATAGTAAC-TCGCACCAATGCCTTCGGG-CTTAGCCCGGA
41732219 CATCATTCGA
Statistics
Matches: 115, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
78 3 0.03
79 71 0.62
80 41 0.36
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (79 bp):
CCTTCGGATCTTAACCCAGATATAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGGAATTAGT
AACTCGCACAAATG
Found at i:41732218 original size:40 final size:40
Alignment explanation
Indices: 41732015--41732218 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
41732005 CGGAATTTAA
* * *
41732015 CCGGATATAGCT-ACTCGCTCAAATGCCTTCTGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41732055 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
41732095 CCAGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41732134 CCAGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
41732174 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
41732214 CCGGA
1 CCGGA
41732219 CATCATTCGA
Statistics
Matches: 140, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 93 0.66
41 12 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:41740156 original size:40 final size:40
Alignment explanation
Indices: 41740071--41740254 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
41740061 GCTACTCGTT
*
41740071 CAAATGCCTTCGGGACATAGCCC-G-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
41740110 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
41740150 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * *
41740189 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
41740230 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41740255 CATCATTCGA
Statistics
Matches: 127, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
38 2 0.02
39 54 0.43
40 58 0.46
41 13 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:41740181 original size:79 final size:79
Alignment explanation
Indices: 41740073--41740254 Score: 235
Period size: 79 Copynumber: 2.3 Consensus size: 79
41740063 TACTCGTTCA
* **
41740073 AATGCCTTCGGGACATAGCCCGTTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGGAT
* *
41740137 TTAGTAAC-TCGCACC
65 ATAGTAACTTAGCA-C
**
41740152 AATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
*
41740216 ATAGTCACTTAGCAC
65 ATAGTAACTTAGCAC
*
41740231 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
41740255 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
78 12 0.13
79 63 0.70
80 15 0.17
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (79 bp):
AATGCCTTCGGGACTTAGCCCGGAATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATA
TAGTAACTTAGCAC
Found at i:41740184 original size:39 final size:40
Alignment explanation
Indices: 41740071--41740254 Score: 225
Period size: 39 Copynumber: 4.7 Consensus size: 40
41740061 GCTACTCGTT
* **
41740071 CAAATGCCTTCGGGACATAGCCCGTTA-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
41740110 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
41740150 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
41740189 CAAATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
41740230 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41740255 CATCATTCGA
Statistics
Matches: 125, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 57 0.46
40 55 0.44
41 11 0.09
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:41751956 original size:14 final size:14
Alignment explanation
Indices: 41751937--41751965 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41751927 CCAATAGTTG
41751937 AGTAATGCTCAAAC
1 AGTAATGCTCAAAC
41751951 AGTAATGCTCAAAC
1 AGTAATGCTCAAAC
41751965 A
1 A
41751966 TTAGTTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
AGTAATGCTCAAAC
Found at i:41755295 original size:71 final size:71
Alignment explanation
Indices: 41755207--41755370 Score: 319
Period size: 71 Copynumber: 2.3 Consensus size: 71
41755197 GAGATGTATC
41755207 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
41755272 AGGACA
66 AGGACA
41755278 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
*
41755343 CGGACA
66 AGGACA
41755349 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
41755371 AGACAAATCG
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 92 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:41765716 original size:39 final size:41
Alignment explanation
Indices: 41765536--41765744 Score: 295
Period size: 40 Copynumber: 5.2 Consensus size: 41
41765526 GCTACTCGCT
* * *
41765536 CAAATGCCTTCGGGACTTAGCCCAG-ATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTAGCA
*
41765576 CAAATGCCTTCGGGACTTAGCCC-GAATATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTAGCA
* *
41765616 CAAATGCCTTCGAGACTTAGCCCGG-ATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTAGCA
* *
41765656 CAAATGGCTTCGGGACTTAGCCCGGAAT-TAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTAGCA
*
41765696 CAAATG-CTTCGGGACTTAGCCCGGAAT-TAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTAGCA
41765735 CAAATGCCTT
1 CAAATGCCTT
41765745 TGTTATCATC
Statistics
Matches: 157, Mismatches: 8, Indels: 8
0.91 0.05 0.05
Matches are distributed among these distances:
39 40 0.25
40 114 0.73
41 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTAGCA
Found at i:41777796 original size:50 final size:50
Alignment explanation
Indices: 41777738--41777915 Score: 187
Period size: 50 Copynumber: 3.5 Consensus size: 50
41777728 CTGATATACG
* *
41777738 TAGTAGCCTGCACTTAGTACTACATACGTGACCTAACCATCTGACACACA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGAAACACA
* * * ** *
41777788 TAGTAGCCTGCACTTAGTACTACACATGCGACCTAACTATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGAAACACA
* * * * * *
41777838 TAGTAGCTTGCATTTAGTACTAAACACGTGACATAAAACCATTTTAAACACA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCT--AACCATCTGAAACACA
*
41777890 TATTAGCCTGCA-TATAGTACTACACA
1 TAGTAGCCTGCACT-TAGTACTACACA
41777916 TGTGTTCTCA
Statistics
Matches: 103, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
50 71 0.69
51 1 0.01
52 31 0.30
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGAAACACA
Found at i:41777867 original size:100 final size:100
Alignment explanation
Indices: 41777707--41777917 Score: 264
Period size: 100 Copynumber: 2.1 Consensus size: 100
41777697 GGGCTGTTAC
* * * *
41777707 ACTACACATGCGACCAAATAACTGATATACGTAGTAGCCTGCACTTAGTACTACATACGTGACCT
1 ACTACACATGCGACCAAATAACTGATACACGTAGTAGCCTGCACTTAGTACTAAACACGTGACAT
*
41777772 -AACCATCTGACACACATAGTAGCCTGCACT-TAGT
66 AAACCATCTGAAACACATAGTAGCCTGCA-TATAGT
* * * * *
41777806 ACTACACATGCGACCTAACTATCTGGTACACGTAGTAGCTTGCATTTAGTACTAAACACGTGACA
1 ACTACACATGCGACC-AAATAACTGATACACGTAGTAGCCTGCACTTAGTACTAAACACGTGACA
* * *
41777871 TAAAACCATTTTAAACACATATTAGCCTGCATATAGT
65 T-AAACCATCTGAAACACATAGTAGCCTGCATATAGT
41777908 ACTACACATG
1 ACTACACATG
41777918 TGTTCTCACA
Statistics
Matches: 95, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
99 15 0.16
100 41 0.43
101 1 0.01
102 38 0.40
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (100 bp):
ACTACACATGCGACCAAATAACTGATACACGTAGTAGCCTGCACTTAGTACTAAACACGTGACAT
AAACCATCTGAAACACATAGTAGCCTGCATATAGT
Found at i:41779231 original size:29 final size:29
Alignment explanation
Indices: 41779189--41779248 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
41779179 CGAAAATCTT
41779189 ACCAGAAGAGTGGTTTAATTATCACATAA
1 ACCAGAAGAGTGGTTTAATTATCACATAA
41779218 ACCAGAAGAGTGGTTTAATTATCACATAA
1 ACCAGAAGAGTGGTTTAATTATCACATAA
41779247 AC
1 AC
41779249 TCCACTATCT
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:0.42, C:0.15, G:0.17, T:0.27
Consensus pattern (29 bp):
ACCAGAAGAGTGGTTTAATTATCACATAA
Found at i:41780567 original size:14 final size:14
Alignment explanation
Indices: 41780548--41780576 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41780538 AAGTTCACTT
41780548 ATTATACTAATCAA
1 ATTATACTAATCAA
41780562 ATTATACTAATCAA
1 ATTATACTAATCAA
41780576 A
1 A
41780577 ATCCATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (14 bp):
ATTATACTAATCAA
Found at i:41782056 original size:21 final size:21
Alignment explanation
Indices: 41782030--41782069 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
41782020 ACCACATTTT
41782030 CAGGCCACACGCCTGTGTCGC
1 CAGGCCACACGCCTGTGTCGC
*
41782051 CAGGCCATACGCCTGTGTC
1 CAGGCCACACGCCTGTGTC
41782070 ACTAGGCCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.40, G:0.28, T:0.17
Consensus pattern (21 bp):
CAGGCCACACGCCTGTGTCGC
Found at i:41782076 original size:21 final size:21
Alignment explanation
Indices: 41782030--41782077 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
41782020 ACCACATTTT
*
41782030 CAGGCCACACGCCTGTGTCGC
1 CAGGCCACACGCCTGTGTCAC
*
41782051 CAGGCCATACGCCTGTGTCAC
1 CAGGCCACACGCCTGTGTCAC
*
41782072 TAGGCC
1 CAGGCC
41782078 GTGTCTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.40, G:0.27, T:0.17
Consensus pattern (21 bp):
CAGGCCACACGCCTGTGTCAC
Found at i:41783426 original size:16 final size:15
Alignment explanation
Indices: 41783400--41783429 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
41783390 AACTGTTTTA
41783400 TTACAAATTTCACTC
1 TTACAAATTTCACTC
41783415 TTACATAATTTCACT
1 TTACA-AATTTCACT
41783430 TACTCCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
TTACAAATTTCACTC
Found at i:41783682 original size:50 final size:51
Alignment explanation
Indices: 41783625--41783768 Score: 173
Period size: 50 Copynumber: 2.8 Consensus size: 51
41783615 GTAACCGAAG
* * *
41783625 CTATCTGGTACGCATAGTAGCCTGCACTTAGTACTGCACATGCAACCT-AA
1 CTATCTGGTACACATAGTAGCCTACACTTAGTACTACACATGCAACCTAAA
* * **
41783675 CTATCTGGTACACGTAATAGCCTACACTTAGTACTACACATGTGACCTAAAA
1 CTATCTGGTACACATAGTAGCCTACACTTAGTACTACACATGCAACCT-AAA
*** *
41783727 CTATCTTAAACACATAGTAGCCTACACATAGTACTACACATG
1 CTATCTGGTACACATAGTAGCCTACACTTAGTACTACACATG
41783769 TGTTCTAACA
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
50 41 0.52
52 38 0.48
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (51 bp):
CTATCTGGTACACATAGTAGCCTACACTTAGTACTACACATGCAACCTAAA
Found at i:41783751 original size:52 final size:50
Alignment explanation
Indices: 41783637--41783770 Score: 160
Period size: 52 Copynumber: 2.6 Consensus size: 50
41783627 ATCTGGTACG
* * ** **
41783637 CATAGTAGCCTGCACTTAGTACTGCACATGCAACCTAACTATCTGGTACA
1 CATAGTAGCCTACACTTAGTACTACACATGTGACCTAACTATCTGAAACA
* * *
41783687 CGTAATAGCCTACACTTAGTACTACACATGTGACCTAAAACTATCTTAAACA
1 CATAGTAGCCTACACTTAGTACTACACATGTGACCT--AACTATCTGAAACA
*
41783739 CATAGTAGCCTACACATAGTACTACACATGTG
1 CATAGTAGCCTACACTTAGTACTACACATGTG
41783771 TTCTAACAAT
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
50 30 0.43
52 40 0.57
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.26
Consensus pattern (50 bp):
CATAGTAGCCTACACTTAGTACTACACATGTGACCTAACTATCTGAAACA
Found at i:41787039 original size:70 final size:71
Alignment explanation
Indices: 41786956--41787118 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
41786946 CGATTTGTCT
41786956 CGTAGCTCTCTTGTCTACATGGTGTCC-TCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
41787020 CTTTCA
66 CTTTCA
*
41787026 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
41787091 CTTTCA
66 CTTTCA
41787097 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
41787119 GATACATCTC
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
70 27 0.30
71 64 0.70
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
CTTTCA
Found at i:41787156 original size:71 final size:70
Alignment explanation
Indices: 41786956--41787152 Score: 249
Period size: 71 Copynumber: 2.8 Consensus size: 70
41786946 CGATTTGTCT
* * * *
41786956 CGTAGCTCTCTTGTCTACATGGTGT-CCTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
41787020 CTTTCA
65 CTTTCA
* * * *
41787026 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
41787091 CTTTCA
65 CTTTCA
* *
41787097 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
41787153 TACAGGGTGT
Statistics
Matches: 117, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
68 22 0.19
69 1 0.01
70 26 0.22
71 68 0.58
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:41821935 original size:40 final size:40
Alignment explanation
Indices: 41821880--41822006 Score: 139
Period size: 40 Copynumber: 3.2 Consensus size: 40
41821870 GAATGCTACT
* *
41821880 CGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATC
* * ** * *
41821920 CGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAACC
1 CGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATC
* * * *
41821960 CGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATC
41822000 C-GGCTAA
1 CGGGCTAA
41822007 ATTCCGAAGA
Statistics
Matches: 68, Mismatches: 19, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
39 5 0.07
40 63 0.93
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATC
Found at i:41829968 original size:40 final size:40
Alignment explanation
Indices: 41829913--41830080 Score: 196
Period size: 40 Copynumber: 4.2 Consensus size: 40
41829903 TGAATGATAC
* *
41829913 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
41829953 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * ** *
41829993 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * * *
41830033 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
41830073 CC-GGCTAA
1 CCGGGCTAA
41830081 ATTCGAAGAA
Statistics
Matches: 106, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
39 6 0.06
40 98 0.92
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:41838300 original size:18 final size:19
Alignment explanation
Indices: 41838277--41838313 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
41838267 TCAAAAAGTT
41838277 ATTTTAATAATAAT-TTTA
1 ATTTTAATAATAATATTTA
*
41838295 ATTTTAATATTAATATTTA
1 ATTTTAATAATAATATTTA
41838314 TTTATCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTAATAATAATATTTA
Found at i:41838316 original size:18 final size:17
Alignment explanation
Indices: 41838275--41838316 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
41838265 GTTCAAAAAG
41838275 TTATTTTAATAATAATT
1 TTATTTTAATAATAATT
*
41838292 TTAATTTTAATATTAATAT
1 TT-ATTTTAATAATAAT-T
41838311 TTATTT
1 TTATTT
41838317 ATCAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.09
18 17 0.77
19 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTTTAATAATAATT
Found at i:41844117 original size:3 final size:3
Alignment explanation
Indices: 41844109--41844133 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41844099 ATTGAATTCC
41844109 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
41844134 AGAAATGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:41844378 original size:6 final size:6
Alignment explanation
Indices: 41844367--41844394 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
41844357 TAATTTTATG
41844367 AATTAA AATTAA AATTAA AATTAA AATT
1 AATTAA AATTAA AATTAA AATTAA AATT
41844395 TTTAACTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
AATTAA
Found at i:41846896 original size:12 final size:12
Alignment explanation
Indices: 41846861--41846890 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
41846851 AACTATTTCT
41846861 TAAAAATACTAA
1 TAAAAATACTAA
41846873 T-AAAATACTAA
1 TAAAAATACTAA
41846884 TAAAAAT
1 TAAAAAT
41846891 TATAATTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (12 bp):
TAAAAATACTAA
Found at i:41846906 original size:18 final size:19
Alignment explanation
Indices: 41846883--41846927 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
41846873 TAAAATACTA
*
41846883 ATAAAAATTATAATTTA-G
1 ATAAAAATTAGAATTTAGG
41846901 ATAAAAA-TAGAATTTAGG
1 ATAAAAATTAGAATTTAGG
*
41846919 AAAAAAATT
1 ATAAAAATT
41846928 TAAGAGATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 8 0.35
18 14 0.61
19 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (19 bp):
ATAAAAATTAGAATTTAGG
Found at i:41850340 original size:49 final size:49
Alignment explanation
Indices: 41850280--41850384 Score: 183
Period size: 49 Copynumber: 2.1 Consensus size: 49
41850270 AATTTTGGGT
* *
41850280 CCACATACCCGTTTGGCCCACATGCCCAAATTGGCTTCACCTGTGTGGC
1 CCACATGCCCGTTTGGCCCACATGCCCAAATTGGCTTCACCCGTGTGGC
*
41850329 CCACATGCCCGTTTGGCGCACATGCCCAAATTGGCTTCACCCGTGTGGC
1 CCACATGCCCGTTTGGCCCACATGCCCAAATTGGCTTCACCCGTGTGGC
41850378 CCACATG
1 CCACATG
41850385 GCCTGGCCCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.18, C:0.37, G:0.22, T:0.23
Consensus pattern (49 bp):
CCACATGCCCGTTTGGCCCACATGCCCAAATTGGCTTCACCCGTGTGGC
Found at i:41852112 original size:29 final size:31
Alignment explanation
Indices: 41852048--41852112 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 31
41852038 ATTTGGTCTT
* *
41852048 ATTTGATTCATTTTAATAGTACAATGATCAA
1 ATTTGATCCATTTTAAGAGTACAATGATCAA
* *
41852079 A-TTGATCCA-TTTAAGAGTAGAGTGA-CAA
1 ATTTGATCCATTTTAAGAGTACAATGATCAA
41852107 ATTTGA
1 ATTTGA
41852113 CCAGATCCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 4 0.14
29 17 0.59
30 7 0.24
31 1 0.03
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (31 bp):
ATTTGATCCATTTTAAGAGTACAATGATCAA
Found at i:41853233 original size:21 final size:21
Alignment explanation
Indices: 41853194--41853233 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
41853184 CCTATTATTT
*
41853194 TGTTCAATTTCTTCGTTTAAG
1 TGTTCAATTGCTTCGTTTAAG
* *
41853215 TGTTCAATTGGTTCTTTTA
1 TGTTCAATTGCTTCGTTTA
41853234 CTTAGGTGAA
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:0.17, C:0.12, G:0.15, T:0.55
Consensus pattern (21 bp):
TGTTCAATTGCTTCGTTTAAG
Found at i:41853657 original size:63 final size:62
Alignment explanation
Indices: 41853569--41853745 Score: 201
Period size: 63 Copynumber: 2.8 Consensus size: 62
41853559 TGGTAGGCCA
* * * **
41853569 TGTAACTCGCTGTTTTGGAATTAGAGTCACATAGGCTAGAGACACGGACGTGTGTCTAAGCCG
1 TGTAACTCACTGTTTTGGAATTAGAGTCACACAGGCTAGAGACA-GGACGTGTATCTAAGAAG
* ** * * * *
41853632 TGTAACTCACTATTTTAAAATTAGAGTCACACGGGCCAGAGACAAGAGCGTGTATCTAGGAAG
1 TGTAACTCACTGTTTTGGAATTAGAGTCACACAGGCTAGAGACAGGA-CGTGTATCTAAGAAG
* *
41853695 TGTAACTCACTGTTTTGGAATTAGAGTCACACAAGCTAGAGGCATGGACGT
1 TGTAACTCACTGTTTTGGAATTAGAGTCACACAGGCTAGAGACA-GGACGT
41853746 ACGTTTAGGT
Statistics
Matches: 92, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
62 2 0.02
63 88 0.96
64 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (62 bp):
TGTAACTCACTGTTTTGGAATTAGAGTCACACAGGCTAGAGACAGGACGTGTATCTAAGAAG
Found at i:41854171 original size:42 final size:42
Alignment explanation
Indices: 41854124--41854208 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
41854114 TCGAATAAGT
41854124 AAGTGTGTTTTGTATTTTATGA-ACATAATCTGAATTCGTATC
1 AAGTGTGTTTTGTATTTTATGAGA-ATAATCTGAATTCGTATC
*
41854166 AAGTGTGTTTTGTATTTTATGAGAATGATCTGAATTCGTATC
1 AAGTGTGTTTTGTATTTTATGAGAATAATCTGAATTCGTATC
41854208 A
1 A
41854209 CTATATATGT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 40 0.98
43 1 0.02
ACGTcount: A:0.28, C:0.08, G:0.19, T:0.45
Consensus pattern (42 bp):
AAGTGTGTTTTGTATTTTATGAGAATAATCTGAATTCGTATC
Found at i:41857581 original size:15 final size:14
Alignment explanation
Indices: 41857528--41857583 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
41857518 GGAAAATTTT
41857528 GAAAAAGTA-AAAGAA
1 GAAAAAG-AGAAAG-A
* *
41857543 GAAAAAAATAAA-A
1 GAAAAAGAGAAAGA
41857556 GAAAAAGAGAAAGA
1 GAAAAAGAGAAAGA
41857570 GAAAATAGAGAAAG
1 GAAAA-AGAGAAAG
41857584 GGAAGAAGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
13 11 0.31
14 7 0.20
15 17 0.49
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.05
Consensus pattern (14 bp):
GAAAAAGAGAAAGA
Found at i:41860759 original size:32 final size:32
Alignment explanation
Indices: 41860705--41860776 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
41860695 ATTTTTATTG
* * *
41860705 TTTTAAATTAAGTACTATTAATAATATAAATA
1 TTTTAAAATAAATACTAATAATAATATAAATA
* *
41860737 TTTTAAAATAAATATTAATAATAATATACATA
1 TTTTAAAATAAATACTAATAATAATATAAATA
41860769 TTTTAAAA
1 TTTTAAAA
41860777 ATGTTTTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (32 bp):
TTTTAAAATAAATACTAATAATAATATAAATA
Found at i:41864530 original size:87 final size:87
Alignment explanation
Indices: 41864373--41864564 Score: 231
Period size: 87 Copynumber: 2.2 Consensus size: 87
41864363 ATAATTTGCG
* ** * ** * * * * *
41864373 ACACTAATGGTTTATCCACGAATTTACTGGTAGCTCTTATCTGCAAGCATGTTGTGTACTCATAA
1 ACACTAATGGTTCATCCAAAAACTTACTGACAACTCTTATCTACAAACACGTTGTGTACTCACAA
*
41864438 TCTACTGGCAGTTTATATGCAA
66 CCTACTGGCAGTTTATATGCAA
* *
41864460 ACACTAATGGTTCATCCAAAAACTTACTGACAACTTTTATCTACAAACACGTTGTGTATTCACAA
1 ACACTAATGGTTCATCCAAAAACTTACTGACAACTCTTATCTACAAACACGTTGTGTACTCACAA
* *
41864525 CCTACTGGTAGTTTATCTGCAA
66 CCTACTGGCAGTTTATATGCAA
*
41864547 ACACTGATGGTTCATCCA
1 ACACTAATGGTTCATCCA
41864565 CAAATTGAAG
Statistics
Matches: 88, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (87 bp):
ACACTAATGGTTCATCCAAAAACTTACTGACAACTCTTATCTACAAACACGTTGTGTACTCACAA
CCTACTGGCAGTTTATATGCAA
Found at i:41865519 original size:46 final size:46
Alignment explanation
Indices: 41865452--41865545 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
41865442 AACATGTAGT
* *
41865452 TGATTGATGATAAAGAGTTGTCATTGATATGGAGTGTTAGAATCAA
1 TGATTGATGATAAAGAGTTGTCATTAATATGGAGTGTCAGAATCAA
41865498 TGATTGATGATAAAGAGTTGTCATTAATATGGAGTGTCAGAATCAA
1 TGATTGATGATAAAGAGTTGTCATTAATATGGAGTGTCAGAATCAA
41865544 TG
1 TG
41865546 CATGAATATG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (46 bp):
TGATTGATGATAAAGAGTTGTCATTAATATGGAGTGTCAGAATCAA
Found at i:41867024 original size:5 final size:5
Alignment explanation
Indices: 41867009--41867079 Score: 61
Period size: 5 Copynumber: 13.8 Consensus size: 5
41866999 TATATCGGAA
* * * * * *
41867009 CATAT CTTAT CATAT CAAAG CATAT TATAAAT CATAC CATAC CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CAT--AT CATAT CATAT CATAT CATAT
*
41867061 CATAT CATAT TATAT CATA
1 CATAT CATAT CATAT CATA
41867080 CCATGCAATG
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
5 48 0.92
7 4 0.08
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.37
Consensus pattern (5 bp):
CATAT
Found at i:41870454 original size:46 final size:47
Alignment explanation
Indices: 41870402--41870698 Score: 241
Period size: 47 Copynumber: 6.4 Consensus size: 47
41870392 GATGTGAACT
*
41870402 AGTGTAAGA-CATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCCACGA-GATGAGAGTC
* * *
41870448 AGTGTAAGACCATGTCTGAGACATGGCATCGG-CATTGAGACGAGAG-C
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCCA-CGAGATGAGAGTC
* * * * * *
41870495 TAGTGTAAGA-CATGTCTAGGACATGTATCAGCCTCGAGACGTA-AGCC
1 -AGTGTAAGACCATGTCTGGGACATGCATCGGCCACGAGATG-AGAGTC
* * * *
41870542 AGTGTAAGA-CATGTCTAGGACATGCATCGACTACGAGATGATAGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCCACGAGATGAGAGTC
* * * * *
41870588 AATGTAAGACCATGTCTGAGACATACATCGGCTACGAGATGATAGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCCACGAGATGAGAGTC
* * * ** * * *
41870635 AATGTAAGACCATGTTTGGGACATGGCATC-GACTTGATATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCCACGAGATGAGAGTC
41870682 AGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTCT
41870699 AGGATATGAC
Statistics
Matches: 205, Mismatches: 35, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
45 1 0.00
46 67 0.33
47 110 0.54
48 26 0.13
49 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGGCCACGAGATGAGAGTC
Found at i:41870657 original size:140 final size:140
Alignment explanation
Indices: 41870402--41870711 Score: 342
Period size: 140 Copynumber: 2.2 Consensus size: 140
41870392 GATGTGAACT
* * * *
41870402 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGTCAGTGTAAGACCATGTCTGA
1 AGTGTAAGACATGTCTAGGACATGCATCGACCACATGATGAGAGTCAATGTAAGACCATGTCTGA
* * * * *
41870467 GACATGGCATCGGCATTGAGACGAGAGCTAGTGTAAGACATGTCTAGGACAT-GTATCAGCCTCG
66 GACATGACATCGGCATCGAGACGAGAGCTAATGTAAGACATGTCTAGGACATGGCATC-GACTCG
41870531 AGACGTAAGCC
130 AGACGTAAGCC
* *
41870542 AGTGTAAGACATGTCTAGGACATGCATCGACTACGA-GATGATAGTCAATGTAAGACCATGTCTG
1 AGTGTAAGACATGTCTAGGACATGCATCGACCAC-ATGATGAGAGTCAATGTAAGACCATGTCTG
* * * *
41870606 AGACAT-ACATCGGC-TACGAGATGATAG-TCAATGTAAGACCATGTTTGGGACATGGCATCGAC
65 AGACATGACATCGGCAT-CGAGACGAGAGCT-AATGTAAGA-CATGTCTAGGACATGGCATCGAC
* * * *
41870668 TTGATATGTGAGCC
127 TCGAGACGTAAGCC
*
41870682 AGTGTAAGACCATGTCTAGGATATGACATC
1 AGTGTAAGA-CATGTCTAGGACATG-CATC
41870712 AGCACCTTAC
Statistics
Matches: 143, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
138 2 0.01
139 23 0.16
140 95 0.66
141 19 0.13
142 4 0.03
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (140 bp):
AGTGTAAGACATGTCTAGGACATGCATCGACCACATGATGAGAGTCAATGTAAGACCATGTCTGA
GACATGACATCGGCATCGAGACGAGAGCTAATGTAAGACATGTCTAGGACATGGCATCGACTCGA
GACGTAAGCC
Found at i:41870696 original size:94 final size:93
Alignment explanation
Indices: 41870392--41870698 Score: 277
Period size: 94 Copynumber: 3.3 Consensus size: 93
41870382 TGGGTCATTT
* * * * * *
41870392 GATGTGAACTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGTCAGTGTAAG
1 GATGTGAGCCAGTGTAAGACATGTCTGAGACATGCATCGGCTACGA-GATGATAGTCAGTGTAAG
* *
41870456 ACCATGTCTGAGACATGGCATCGGCATTGA
65 ACCATGTCTGGGACATGGCATCGAC-TTGA
* * * * * * *
41870486 GACGAGAGCTAGTGTAAGACATGTCT-AGGACATGTATCAGCCT-CGAGACG-TAAGCCAGTGTA
1 GATGTGAGCCAGTGTAAGACATGTCTGA-GACATGCATC-GGCTACGAGATGAT-AGTCAGTGTA
* *
41870548 AGA-CATGTCTAGGACAT-GCATCGACTACGA
63 AGACCATGTCTGGGACATGGCATCGACT-TGA
* * * *
41870578 GATGAT-AGTCAATGTAAGACCATGTCTGAGACATACATCGGCTACGAGATGATAGTCAATGTAA
1 GATG-TGAGCCAGTGTAAGA-CATGTCTGAGACATGCATCGGCTACGAGATGATAGTCAGTGTAA
*
41870642 GACCATGTTTGGGACATGGCATCGACTTGA
64 GACCATGTCTGGGACATGGCATCGACTTGA
*
41870672 TATGTGAGCCAGTGTAAGACCATGTCT
1 GATGTGAGCCAGTGTAAGA-CATGTCT
41870699 AGGATATGAC
Statistics
Matches: 168, Mismatches: 32, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
91 1 0.01
92 25 0.15
93 45 0.27
94 85 0.51
95 12 0.07
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (93 bp):
GATGTGAGCCAGTGTAAGACATGTCTGAGACATGCATCGGCTACGAGATGATAGTCAGTGTAAGA
CCATGTCTGGGACATGGCATCGACTTGA
Found at i:41874752 original size:34 final size:34
Alignment explanation
Indices: 41874714--41874781 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
41874704 TCATATCTGA
* * *
41874714 TACTGAAACCGAAATGGGCTAAGGCTCGAACTGC
1 TACTGAAACCAAAATGGGCTAAGGCCCAAACTGC
* *
41874748 TACTGAAACTAAAATGGGCTTAGGCCCAAACTGC
1 TACTGAAACCAAAATGGGCTAAGGCCCAAACTGC
41874782 ATTTGACTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.19
Consensus pattern (34 bp):
TACTGAAACCAAAATGGGCTAAGGCCCAAACTGC
Found at i:41879531 original size:17 final size:17
Alignment explanation
Indices: 41879509--41879542 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41879499 GTTCATTCAG
*
41879509 AATTAAATCAGCCACCC
1 AATTAAAACAGCCACCC
41879526 AATTAAAACAGCCACCC
1 AATTAAAACAGCCACCC
41879543 TTTCAGTAGA
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:0.35, G:0.06, T:0.15
Consensus pattern (17 bp):
AATTAAAACAGCCACCC
Found at i:41883654 original size:23 final size:23
Alignment explanation
Indices: 41883597--41883654 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
41883587 CGATCTATGC
* *
41883597 CAGAAGAAAGAACGTGTCAAAAGA
1 CAGAA-AAAGAGCGTGCCAAAAGA
*
41883621 CAGAGAAAGAGCGTGCCAAAAGA
1 CAGAAAAAGAGCGTGCCAAAAGA
41883644 CAGAAAAAGAG
1 CAGAAAAAGAG
41883655 TTGTTTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 26 0.87
24 4 0.13
ACGTcount: A:0.53, C:0.14, G:0.28, T:0.05
Consensus pattern (23 bp):
CAGAAAAAGAGCGTGCCAAAAGA
Found at i:41884364 original size:16 final size:17
Alignment explanation
Indices: 41884341--41884378 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
41884331 TGAAAACATG
41884341 ATTTTTTTTCTTTATAA
1 ATTTTTTTTCTTTATAA
41884358 ATTTTTTTTCTTTATAA
1 ATTTTTTTTCTTTATAA
41884375 ATTT
1 ATTT
41884379 GGAAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTTTCTTTATAA
Found at i:41887204 original size:13 final size:14
Alignment explanation
Indices: 41887186--41887214 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
41887176 ATAATTATTC
41887186 AAATATAGT-TTTA
1 AAATATAGTATTTA
41887199 AAATATAGTATTTA
1 AAATATAGTATTTA
41887213 AA
1 AA
41887215 TAAGATTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
AAATATAGTATTTA
Found at i:41888948 original size:23 final size:23
Alignment explanation
Indices: 41888922--41888968 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
41888912 CATGTTAAAT
41888922 TATTAATATGTGATTTTTCACTA
1 TATTAATATGTGATTTTTCACTA
41888945 TATTAATATGTGATTTTTCACTA
1 TATTAATATGTGATTTTTCACTA
41888968 T
1 T
41888969 GTAGGAGGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.53
Consensus pattern (23 bp):
TATTAATATGTGATTTTTCACTA
Found at i:41892156 original size:6 final size:6
Alignment explanation
Indices: 41892145--41892178 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
41892135 GTGATGTGGT
*
41892145 AATGGG AATGGG AATGGG AATAGG AATGGG AATG
1 AATGGG AATGGG AATGGG AATGGG AATGGG AATG
41892179 AACATGTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.44, T:0.18
Consensus pattern (6 bp):
AATGGG
Done.