Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 7 of 172
Found at i:2045684 original size:15 final size:15
Alignment explanation
Indices: 2045656--2045698 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
2045646 TGTTTGTTTG
2045656 CTAGTAAAAT-ATTTT
1 CTAG-AAAATGATTTT
2045671 CTAGAAAATGA-TTT
1 CTAGAAAATGATTTT
*
2045685 CTGGAAAATGATTT
1 CTAGAAAATGATTT
2045699 ACTTTTCTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.40
Consensus pattern (15 bp):
CTAGAAAATGATTTT
Found at i:2045714 original size:19 final size:20
Alignment explanation
Indices: 2045682--2045727 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
2045672 TAGAAAATGA
2045682 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
2045702 TTTCTGG-AAATGATTTACT
1 TTTCTGGAAAATGATTTACT
2045721 TTTCTGG
1 TTTCTGG
2045728 TGTTTAGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:2045829 original size:18 final size:18
Alignment explanation
Indices: 2045803--2045845 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2045793 AAAAGTTGTT
*
2045803 TTTACATATATTAATAAA
1 TTTATATATATTAATAAA
2045821 TTTATATATATTAATAAA
1 TTTATATATATTAATAAA
*
2045839 ATTATAT
1 TTTATAT
2045846 TTTTAATAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTATATATATTAATAAA
Found at i:2051177 original size:25 final size:25
Alignment explanation
Indices: 2051149--2051198 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2051139 GGAAGAGAAG
*
2051149 ATGAAGAATGGAAGAAGGAAAAGGA
1 ATGAAGAAGGGAAGAAGGAAAAGGA
*
2051174 ATGAAGAAGGGAAGAAGGAGAAGGA
1 ATGAAGAAGGGAAGAAGGAAAAGGA
2051199 GCCTTACCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.40, T:0.06
Consensus pattern (25 bp):
ATGAAGAAGGGAAGAAGGAAAAGGA
Found at i:2052034 original size:42 final size:41
Alignment explanation
Indices: 2051958--2052041 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 41
2051948 TTCTGAGGTG
* * *
2051958 TGATTTCGTGTAAGACCATGTTTGGGACATTGGCATCGCATA
1 TGATTTCGTGTAAGACCATGTCTGAGACAGTGGCATCG-ATA
* *
2052000 TGATTTCGTGTAAGACCCTGTCTGAGATAGTGGCATCGATA
1 TGATTTCGTGTAAGACCATGTCTGAGACAGTGGCATCGATA
2052041 T
1 T
2052042 ATTATAACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 4 0.11
42 33 0.89
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (41 bp):
TGATTTCGTGTAAGACCATGTCTGAGACAGTGGCATCGATA
Found at i:2057589 original size:48 final size:48
Alignment explanation
Indices: 2057485--2057589 Score: 131
Period size: 48 Copynumber: 2.2 Consensus size: 48
2057475 TGATGATATG
* * * *
2057485 ATGTTGTCCAAATTGGTGCTTAATTGCTGTACATTTTTGAGTATATTA
1 ATGTTGTCCAAATTGGTGCTTAAATGCTGTACATTTTTGAGCAAATCA
* * *
2057533 ATGCTGTCCAAATTGGTGCTTAAATGTTGTCCATTTTTGTA-CAAATCA
1 ATGTTGTCCAAATTGGTGCTTAAATGCTGTACATTTTTG-AGCAAATCA
2057581 ATGTTGTCC
1 ATGTTGTCC
2057590 GAATATTGTT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
48 47 0.98
49 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (48 bp):
ATGTTGTCCAAATTGGTGCTTAAATGCTGTACATTTTTGAGCAAATCA
Found at i:2058809 original size:34 final size:34
Alignment explanation
Indices: 2058770--2058837 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
2058760 GTTGAAGAAA
2058770 GTTCACCTTGCGTCCTTTATTGAGCCAACTATGT
1 GTTCACCTTGCGTCCTTTATTGAGCCAACTATGT
2058804 GTTCACCTTGCGTCCTTTATTGAGCCAACTATGT
1 GTTCACCTTGCGTCCTTTATTGAGCCAACTATGT
2058838 ATAAAACCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (34 bp):
GTTCACCTTGCGTCCTTTATTGAGCCAACTATGT
Found at i:2063063 original size:17 final size:17
Alignment explanation
Indices: 2063031--2063063 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2063021 ACAAAAATTC
2063031 ATCCTAAAAAACAAAAT
1 ATCCTAAAAAACAAAAT
2063048 ATCCATAAAAAA-AAAA
1 ATCC-TAAAAAACAAAA
2063064 ACTGCTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (17 bp):
ATCCTAAAAAACAAAAT
Found at i:2063064 original size:18 final size:17
Alignment explanation
Indices: 2063031--2063064 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2063021 ACAAAAATTC
*
2063031 ATCCTAAAAAACAAAAT
1 ATCCTAAAAAAAAAAAT
2063048 ATCCATAAAAAAAAAAA
1 ATCC-TAAAAAAAAAAA
2063065 CTGCTAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.71, C:0.15, G:0.00, T:0.15
Consensus pattern (17 bp):
ATCCTAAAAAAAAAAAT
Found at i:2080375 original size:52 final size:51
Alignment explanation
Indices: 2080304--2080558 Score: 305
Period size: 46 Copynumber: 5.1 Consensus size: 51
2080294 ATCAAGTGAC
* **
2080304 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-G
* *
2080356 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGT---AA-T-
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
2080402 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-G
* * *
2080454 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGAGAC-----
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
** *
2080500 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAGAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACA-AGTG
2080552 ATAAGTG
1 A-AAGTG
2080559 GCTACACTTA
Statistics
Matches: 176, Mismatches: 14, Indels: 25
0.82 0.07 0.12
Matches are distributed among these distances:
46 83 0.47
48 1 0.01
49 4 0.02
50 1 0.01
52 82 0.47
53 5 0.03
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:2080413 original size:98 final size:98
Alignment explanation
Indices: 2080290--2080551 Score: 445
Period size: 98 Copynumber: 2.7 Consensus size: 98
2080280 TTTGAGTACT
* *
2080290 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTAACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
2080355 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* **
2080388 TCTGATCAAGTAATAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTAACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
2080453 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
*
2080486 TCTGATCAAG-AGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAGAG
1 TCTGATCAAGTA-ACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACA-AG
2080550 TG
64 TG
2080552 ATAAGTGGCT
Statistics
Matches: 153, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
97 1 0.01
98 148 0.97
99 4 0.03
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (98 bp):
TCTGATCAAGTAACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:2080565 original size:37 final size:36
Alignment explanation
Indices: 2080522--2080630 Score: 166
Period size: 37 Copynumber: 3.0 Consensus size: 36
2080512 GATAGCTTTA
2080522 GCTACACTTATCTGATCAAGAGACAGAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACA-AGTGATAAGTG
* *
2080559 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAGAC-AAGTGATAAGTG
*
2080596 GCTACACTTATCTGATC-AGGGACAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAGTGATAAGTG
2080631 ATCATACGTA
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
35 11 0.17
36 4 0.06
37 50 0.76
38 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.25
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGAGACAAGTGATAAGTG
Found at i:2088778 original size:18 final size:17
Alignment explanation
Indices: 2088756--2088790 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2088746 TTATTATTAA
*
2088756 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
2088774 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
2088791 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:2091643 original size:33 final size:33
Alignment explanation
Indices: 2091604--2091667 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
2091594 ATTATAAAGC
2091604 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
2091637 ATGTATAATTGACCTAAAATTAATTGTTGGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGT
2091668 NNNNNNNNNN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.42
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTGT
Found at i:2093069 original size:23 final size:23
Alignment explanation
Indices: 2093043--2093117 Score: 141
Period size: 23 Copynumber: 3.3 Consensus size: 23
2093033 TAAACAAATT
2093043 CAATTTCCAGCAGACAATCAAAA
1 CAATTTCCAGCAGACAATCAAAA
*
2093066 CAATTTCCAGCAGACAATCATAA
1 CAATTTCCAGCAGACAATCAAAA
2093089 CAATTTCCAGCAGACAATCAAAA
1 CAATTTCCAGCAGACAATCAAAA
2093112 CAATTT
1 CAATTT
2093118 TAGAACAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.45, C:0.25, G:0.08, T:0.21
Consensus pattern (23 bp):
CAATTTCCAGCAGACAATCAAAA
Found at i:2094081 original size:32 final size:34
Alignment explanation
Indices: 2094040--2094103 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
2094030 CTTTTCTATT
* *
2094040 TTCTTTTAA-GAGAATGGTTTTATAAT-GTGACA
1 TTCTTTTAAGGAAAATAGTTTTATAATAGTGACA
2094072 TTCTTTTAAGGAAAATAGTTTTATAATAGTGA
1 TTCTTTTAAGGAAAATAGTTTTATAATAGTGA
2094104 AATTATTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 9 0.32
33 15 0.54
34 4 0.14
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (34 bp):
TTCTTTTAAGGAAAATAGTTTTATAATAGTGACA
Found at i:2094451 original size:17 final size:17
Alignment explanation
Indices: 2094431--2094466 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2094421 ACTCAAAGGG
*
2094431 AAATAAATAGCAAAAGA
1 AAATAAACAGCAAAAGA
*
2094448 AAATAAACAGCAATAGA
1 AAATAAACAGCAAAAGA
2094465 AA
1 AA
2094467 CATGCAATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.08, G:0.11, T:0.11
Consensus pattern (17 bp):
AAATAAACAGCAAAAGA
Found at i:2106871 original size:3 final size:3
Alignment explanation
Indices: 2106863--2107005 Score: 286
Period size: 3 Copynumber: 47.7 Consensus size: 3
2106853 TTAAGAGCTG
2106863 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2106911 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2106959 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2107006 GGGAATTGTC
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 140 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2107803 original size:7 final size:7
Alignment explanation
Indices: 2107788--2107819 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
2107778 GGATTATAGA
2107788 TTTGAAGT
1 TTTG-AGT
2107796 TTTGAGT
1 TTTGAGT
2107803 TTTGAGT
1 TTTGAGT
2107810 TTTGAGT
1 TTTGAGT
2107817 TTT
1 TTT
2107820 TTATTTGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.16, C:0.00, G:0.25, T:0.59
Consensus pattern (7 bp):
TTTGAGT
Found at i:2124385 original size:12 final size:12
Alignment explanation
Indices: 2124368--2124392 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2124358 ACTTTGGTAG
2124368 TGTTTTGGTGAT
1 TGTTTTGGTGAT
2124380 TGTTTTGGTGAT
1 TGTTTTGGTGAT
2124392 T
1 T
2124393 CTCTTTCCAT
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:0.08, C:0.00, G:0.32, T:0.60
Consensus pattern (12 bp):
TGTTTTGGTGAT
Found at i:2134752 original size:13 final size:13
Alignment explanation
Indices: 2134734--2134760 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2134724 AAAGGATCTA
2134734 ATTATGGAACTTC
1 ATTATGGAACTTC
2134747 ATTATGGAACTTC
1 ATTATGGAACTTC
2134760 A
1 A
2134761 AGCGTAACTC
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:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (13 bp):
ATTATGGAACTTC
Found at i:2159053 original size:42 final size:42
Alignment explanation
Indices: 2158954--2159056 Score: 156
Period size: 42 Copynumber: 2.5 Consensus size: 42
2158944 CGGCTATATG
* *
2158954 AACG-GCACTAAGTGTACAAAATTAAAATGATGATGTTGAAT
1 AACGAGCACTAAGTGTGCGAAATTAAAATGATGATGTTGAAT
*
2158995 AA-TAGGCACTAAGTGTGCGAAATTAAAATGATGATGTTGAAT
1 AACGA-GCACTAAGTGTGCGAAATTAAAATGATGATGTTGAAT
2159037 AACGAGCACTAAGTGTGCGA
1 AACGAGCACTAAGTGTGCGA
2159057 TACCGAGAGC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
41 2 0.04
42 52 0.95
43 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (42 bp):
AACGAGCACTAAGTGTGCGAAATTAAAATGATGATGTTGAAT
Found at i:2159861 original size:3 final size:3
Alignment explanation
Indices: 2159853--2159879 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2159843 ATTTGATCGA
2159853 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
2159880 GAAATTTCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2161230 original size:40 final size:40
Alignment explanation
Indices: 2161147--2161250 Score: 102
Period size: 40 Copynumber: 2.6 Consensus size: 40
2161137 TTTTGCGGCG
* ** * *
2161147 TTTTTCAAAAAGCGTCGCTAATGCTCGATCTATAGCGTCA
1 TTTTCCAAAAAGCACCGCTAATGCTCGACCTATAACGTCA
* * * *
2161187 TTTTCCAATAAGCGCTGCTAATGCTTGACCTATAACGGT-A
1 TTTTCCAAAAAGCACCGCTAATGCTCGACCTATAAC-GTCA
*
2161227 TTTTTCAAAAAGCACCGCTAATGC
1 TTTTCCAAAAAGCACCGCTAATGC
2161251 CACTAAAGCT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
40 50 0.96
41 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (40 bp):
TTTTCCAAAAAGCACCGCTAATGCTCGACCTATAACGTCA
Found at i:2161362 original size:40 final size:40
Alignment explanation
Indices: 2161302--2161432 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 40
2161292 TTTTGCAGCA
** * *
2161302 TTTTTCAAAAAGCGTTGCTAATGGTCGACCTATAGCGGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCG
* **
2161342 TTTTCCAAAAAGCGCCGCTAATGCTCGATCTATAATGGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCG
* * * *
2161382 TTTTTCAAAGAGCACCACTAATGCTCGATCTATAGCGACG
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCG
2161422 TTTTTCAAAAA
1 TTTTTCAAAAA
2161433 TCTTCGCTAA
Statistics
Matches: 76, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 76 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (40 bp):
TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCG
Found at i:2169009 original size:28 final size:31
Alignment explanation
Indices: 2168978--2169046 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
2168968 ATTTTTCAAG
*
2168978 TTTTTAAAATT-TTAATTAAA-T-TTATTAA
1 TTTTTAAAATTATAAATTAAATTATTATTAA
* * *
2169006 TTTTTTATATTATAAATTAAATTATTGTTAA
1 TTTTTAAAATTATAAATTAAATTATTATTAA
*
2169037 TTATTAAAAT
1 TTTTTAAAAT
2169047 AAAATATTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
28 9 0.29
29 8 0.26
30 1 0.03
31 13 0.42
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (31 bp):
TTTTTAAAATTATAAATTAAATTATTATTAA
Found at i:2174980 original size:2 final size:2
Alignment explanation
Indices: 2174973--2175004 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2174963 AATTCACCAT
2174973 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2175005 GCATACATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2183783 original size:19 final size:20
Alignment explanation
Indices: 2183737--2183788 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
2183727 AAAGAAAAAA
* *
2183737 ATTTTAATTTTCCTATTATT
1 ATTTTATTTTTACTATTATT
2183757 ATTATTTATTTTTACTATT-TT
1 A-T-TTTATTTTTACTATTATT
2183778 ATTTTATTTTT
1 ATTTTATTTTT
2183789 GTAGGAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 9 0.32
20 2 0.07
21 4 0.14
22 13 0.46
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTTATTTTTACTATTATT
Found at i:2197657 original size:25 final size:25
Alignment explanation
Indices: 2197623--2197671 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2197613 CACAAAGCAA
**
2197623 ATTAATTTTTTTTATTAAAATTTTC
1 ATTAATTTTTACTATTAAAATTTTC
2197648 ATTAATTTTTACTATTAAAATTTT
1 ATTAATTTTTACTATTAAAATTTT
2197672 ACATAACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTAATTTTTACTATTAAAATTTTC
Found at i:2203592 original size:17 final size:18
Alignment explanation
Indices: 2203567--2203604 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2203557 AATAATTATA
* *
2203567 TTTATTTTTTAAAT-TTT
1 TTTAATTTTAAAATATTT
2203584 TTTAATTTTAAAATATTT
1 TTTAATTTTAAAATATTT
2203602 TTT
1 TTT
2203605 TTTATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTAATTTTAAAATATTT
Found at i:2203601 original size:28 final size:29
Alignment explanation
Indices: 2203569--2203651 Score: 107
Period size: 28 Copynumber: 2.9 Consensus size: 29
2203559 TAATTATATT
2203569 TATTTTTTAAAT-TTTTTTAATTTTAAAA
1 TATTTTTTAAATATTTTTTAATTTTAAAA
**
2203597 TATTTTTT-TTTATTTTTTAATTTTAAAA
1 TATTTTTTAAATATTTTTTAATTTTAAAA
*
2203625 TATTTTTAAAATACTTTTTTAAATTTT
1 TATTTTTTAAATA-TTTTTT-AATTTT
2203652 TTTAATTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
27 1 0.02
28 31 0.67
29 2 0.04
30 6 0.13
31 6 0.13
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (29 bp):
TATTTTTTAAATATTTTTTAATTTTAAAA
Found at i:2203631 original size:11 final size:11
Alignment explanation
Indices: 2203617--2203656 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
2203607 TATTTTTTAA
2203617 TTTTAAAATAT
1 TTTTAAAATAT
2203628 TTTTAAAATACT
1 TTTTAAAATA-T
* *
2203640 TTTTTAAATTT
1 TTTTAAAATAT
2203651 TTTTAA
1 TTTTAA
2203657 TTTTAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:2203632 original size:39 final size:40
Alignment explanation
Indices: 2203589--2203664 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 40
2203579 ATTTTTTTAA
* **
2203589 TTTTAAAATATTTTTTTTTA-TTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAATAT
2203628 TTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAA
1 TTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAA
2203665 ATAAATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 17 0.52
40 16 0.48
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (40 bp):
TTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAATAT
Found at i:2220943 original size:44 final size:46
Alignment explanation
Indices: 2220858--2220950 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 46
2220848 GGTTCGCTGA
* *
2220858 AATGAAATAGAGGCGTAATGGGTAATTCTTTTATTTGGTTGAATGG
1 AATGAAATAGAGGCGTAATGAGTAATTCTTGTATTTGGTTGAATGG
* *
2220904 AATGGAATAGAGGCGTAAT-AGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGAAATAGAGGCGTAATGAGTAATTCTTGTATTTGGTTGAATGG
2220948 AAT
1 AAT
2220951 AGAGGTGTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 23 0.53
45 2 0.05
46 18 0.42
ACGTcount: A:0.30, C:0.04, G:0.29, T:0.37
Consensus pattern (46 bp):
AATGAAATAGAGGCGTAATGAGTAATTCTTGTATTTGGTTGAATGG
Found at i:2233248 original size:6 final size:6
Alignment explanation
Indices: 2233237--2233265 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2233227 AAAGACTAAC
2233237 CTCCTG CTCCTG CTCCTG CTCCTG CTCCT
1 CTCCTG CTCCTG CTCCTG CTCCTG CTCCT
2233266 ACTACTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.14, T:0.34
Consensus pattern (6 bp):
CTCCTG
Found at i:2236066 original size:21 final size:21
Alignment explanation
Indices: 2236041--2236084 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2236031 ATCTTCGAGG
2236041 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
2236062 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
2236083 AT
1 AT
2236085 GTAATCTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:2236090 original size:19 final size:19
Alignment explanation
Indices: 2236040--2236095 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
2236030 AATCTTCGAG
2236040 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2236059 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
2236080 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
2236096 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.44
21 19 0.56
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:2236102 original size:22 final size:23
Alignment explanation
Indices: 2236053--2236118 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
2236043 ATGCAATCTT
*
2236053 AGATATGATATATGCAATCTT---
1 AGATATGAT-TATGTAATCTTAGA
2236074 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
2236096 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
2236119 GATTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 10 0.26
21 8 0.21
22 8 0.21
23 13 0.33
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:2236128 original size:22 final size:23
Alignment explanation
Indices: 2236084--2236128 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2236074 AGATATGATA
*
2236084 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
2236107 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
2236129 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:2236315 original size:19 final size:21
Alignment explanation
Indices: 2236291--2236329 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
2236281 GGCTTACTGT
*
2236291 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
2236310 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
2236330 TTAAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:2236605 original size:12 final size:11
Alignment explanation
Indices: 2236536--2236607 Score: 56
Period size: 12 Copynumber: 6.3 Consensus size: 11
2236526 GCCTTTACTA
*
2236536 ATTAATTTATT
1 ATTATTTTATT
*
2236547 ATTATTAT-TT
1 ATTATTTTATT
**
2236557 ATTAATCCTATT
1 ATT-ATTTTATT
*
2236569 ATTATTTGTACT
1 ATTATTT-TATT
2236581 ATTATTGTTATT
1 ATTATT-TTATT
2236593 ATTATTTTCATT
1 ATTATTTT-ATT
2236605 ATT
1 ATT
2236608 TCTTCTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
10 5 0.10
11 13 0.27
12 29 0.60
13 1 0.02
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:2252994 original size:93 final size:92
Alignment explanation
Indices: 2252835--2253003 Score: 225
Period size: 93 Copynumber: 1.8 Consensus size: 92
2252825 AACTATTTTT
* * * * * *
2252835 ATAAAATGTCTAATGTGGCATTTTTATTTTGAAAATGTTCAATGTGGTACTTGAATTATAAATAT
1 ATAAAATGTCCAATATGGCATATGTATTTTGAAAATGTCCAATGTAGTACTTGAATTATAAATAT
2252900 GTGTTTTTATTATGGTACCTATACTTTC
66 GTG-TTTTATTATGGTACCTATACTTTC
* *
2252928 ATAAAATGTCCAATATGGTATATGTATTTT-ACAAATGTCCAATGTAGTACTTGAACTT-TCAAT
1 ATAAAATGTCCAATATGGCATATGTATTTTGA-AAATGTCCAATGTAGTACTTGAA-TTATAAAT
2252991 ATGTGTTTTATTA
64 ATGTGTTTTATTA
2253004 CGGCACATGG
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
92 9 0.14
93 55 0.83
94 2 0.03
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.44
Consensus pattern (92 bp):
ATAAAATGTCCAATATGGCATATGTATTTTGAAAATGTCCAATGTAGTACTTGAATTATAAATAT
GTGTTTTATTATGGTACCTATACTTTC
Found at i:2254663 original size:16 final size:18
Alignment explanation
Indices: 2254634--2254666 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2254624 TCGATGAGAT
2254634 ATAACAAAATATTAAAAA
1 ATAACAAAATATTAAAAA
2254652 ATAA-AAAA-ATTAAAA
1 ATAACAAAATATTAAAA
2254667 TCATATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (18 bp):
ATAACAAAATATTAAAAA
Found at i:2256091 original size:19 final size:20
Alignment explanation
Indices: 2256063--2256101 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2256053 TACTAGTGAT
*
2256063 TACATGTGTAAAT-TTAATA
1 TACATATGTAAATATTAATA
*
2256082 TACATATGTATATATTAATA
1 TACATATGTAAATATTAATA
2256102 AAATAGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (20 bp):
TACATATGTAAATATTAATA
Found at i:2256885 original size:12 final size:13
Alignment explanation
Indices: 2256868--2256897 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2256858 AATAAACATT
2256868 TACAAATAT-ATA
1 TACAAATATAATA
2256880 TACAAATATAATA
1 TACAAATATAATA
2256893 TACAA
1 TACAA
2256898 GTAAATTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (13 bp):
TACAAATATAATA
Found at i:2256983 original size:21 final size:21
Alignment explanation
Indices: 2256945--2256987 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2256935 AAATAAAAAC
*
2256945 AAATAGAAATACATGTATTAAA
1 AAATAGAAATACAAGTA-TAAA
*
2256967 AAATAG-AATAGAAGTATAAA
1 AAATAGAAATACAAGTATAAA
2256987 A
1 A
2256988 GTATGCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.26
21 8 0.42
22 6 0.32
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.23
Consensus pattern (21 bp):
AAATAGAAATACAAGTATAAA
Found at i:2257246 original size:17 final size:17
Alignment explanation
Indices: 2257217--2257251 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2257207 TAAAGTATAT
2257217 AAAGAAAATTAAAAAAA
1 AAAGAAAATTAAAAAAA
2257234 AAAGTAAAA-TAAAAAAA
1 AAAG-AAAATTAAAAAAA
2257251 A
1 A
2257252 GTATGCATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (17 bp):
AAAGAAAATTAAAAAAA
Found at i:2257248 original size:18 final size:17
Alignment explanation
Indices: 2257217--2257251 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2257207 TAAAGTATAT
*
2257217 AAAGAAAATTAAAAAAA
1 AAAGAAAATAAAAAAAA
2257234 AAAGTAAAATAAAAAAAA
1 AAAG-AAAATAAAAAAAA
2257252 GTATGCATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (17 bp):
AAAGAAAATAAAAAAAA
Found at i:2269774 original size:18 final size:17
Alignment explanation
Indices: 2269741--2269779 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2269731 TTGTATAAAT
2269741 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
2269759 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
2269776 TGTG
1 TGTG
2269780 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:2270032 original size:23 final size:23
Alignment explanation
Indices: 2270005--2270102 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
2269995 AGTGTTATTG
2270005 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
2270028 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2270051 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2270073 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2270096 ATCAGTG
1 ATCAGTG
2270103 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:2270071 original size:45 final size:45
Alignment explanation
Indices: 2270007--2270095 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
2269997 TGTTATTGAT
* *
2270007 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
2270052 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
2270096 ATCAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:2281434 original size:219 final size:219
Alignment explanation
Indices: 2281055--2281460 Score: 686
Period size: 219 Copynumber: 1.9 Consensus size: 219
2281045 ATCGTCTTCA
* * *
2281055 TCGCTGTTGTATATCGAAACCTAGGCAAGTCATTGGAATCCTCTGTTTCAACCTCATTGTGGGCT
1 TCGCTGTTCTATATCGAAACCTAGGCAAGTCATTGGAATCCTCTGTTTCAACCACATTGTGGACT
* *
2281120 TCCCCTTCGTCCAGTTCCATGTCTATCATTTTGCTTCTGTATATCGGCTGTGAGTTTGGACACTC
66 TCCCCTTCGTCCAGTTCCATGTCTATCATTTTGCTTCTGTATATCCGCCGTGAGTTTGGACACTC
2281185 ATTGACACTGGGTTCCGCCTTTTCTCCATTTTCAGACCCCGTTGCAGCAGCAGCCATCGTCTTCA
131 ATTGACACTGGGTTCCGCCTTTTCTCCATTTTCAGACCCCGTTGCAGCAGCAGCCATCGTCTTCA
2281250 TCGACTTAAACGTTCGACGGCTGG
196 TCGACTTAAACGTTCGACGGCTGG
*
2281274 TCGCTGTTCTATATCGAAACCTAGTCAAGTCATTGGAATCCTCTGTTTCAACCACATTGTGGACT
1 TCGCTGTTCTATATCGAAACCTAGGCAAGTCATTGGAATCCTCTGTTTCAACCACATTGTGGACT
* * * * *
2281339 TTCCCTTTGTCCAGTTCCATGTCTATCCTTTTGCTTCTGTATGTCCGCCGTGAGTTTGGCCACTC
66 TCCCCTTCGTCCAGTTCCATGTCTATCATTTTGCTTCTGTATATCCGCCGTGAGTTTGGACACTC
* * *
2281404 ATTGACTCTGGGTTTCGCCTTTTCTCCATTTTCAGACCCTGTTGCAGCAGCAGCCAT
131 ATTGACACTGGGTTCCGCCTTTTCTCCATTTTCAGACCCCGTTGCAGCAGCAGCCAT
2281461 TGGTTGAACC
Statistics
Matches: 173, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
219 173 1.00
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.35
Consensus pattern (219 bp):
TCGCTGTTCTATATCGAAACCTAGGCAAGTCATTGGAATCCTCTGTTTCAACCACATTGTGGACT
TCCCCTTCGTCCAGTTCCATGTCTATCATTTTGCTTCTGTATATCCGCCGTGAGTTTGGACACTC
ATTGACACTGGGTTCCGCCTTTTCTCCATTTTCAGACCCCGTTGCAGCAGCAGCCATCGTCTTCA
TCGACTTAAACGTTCGACGGCTGG
Found at i:2282197 original size:11 final size:12
Alignment explanation
Indices: 2282183--2282211 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2282173 TTAAATAATA
2282183 ATTTAATA-TTT
1 ATTTAATATTTT
2282194 ATTTAATATTTT
1 ATTTAATATTTT
2282206 ATTTAA
1 ATTTAA
2282212 AATAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTTAATATTTT
Found at i:2282898 original size:54 final size:54
Alignment explanation
Indices: 2282831--2283009 Score: 171
Period size: 55 Copynumber: 3.2 Consensus size: 54
2282821 TAATTATTTT
* *
2282831 TATGTTTAGATCGATTGTTAGGTCGGAATGCTGCTTATTTTG-ATAGATTGTTTA
1 TATGTTTAAATCGATTGTTAGGT-GGAATGCTGCTTATTTTGAATTGATTGTTTA
* * *
2282885 TATGTTTAAATCGATTGTTATGGTGGAATACTGCTTCTTCTTTTGAATTGATTGTGTA
1 TATGTTTAAATCGATTGTTA-GGTGG-A-A-TGCTGCTTATTTTGAATTGATTGTTTA
* * ** * * * **
2282943 TATGTTTAGATGGATTGTTATATTGGAATACTGGTTGTTTTGAATTGATAATTTA
1 TATGTTTAAATCGATTGTTA-GGTGGAATGCTGCTTATTTTGAATTGATTGTTTA
2282998 TATGTTTAAATC
1 TATGTTTAAATC
2283010 CATTATTACG
Statistics
Matches: 102, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
54 21 0.21
55 34 0.33
56 2 0.02
57 13 0.13
58 32 0.31
ACGTcount: A:0.25, C:0.06, G:0.21, T:0.48
Consensus pattern (54 bp):
TATGTTTAAATCGATTGTTAGGTGGAATGCTGCTTATTTTGAATTGATTGTTTA
Found at i:2282959 original size:58 final size:57
Alignment explanation
Indices: 2282831--2282975 Score: 172
Period size: 58 Copynumber: 2.6 Consensus size: 57
2282821 TAATTATTTT
*
2282831 TATGTTTAGATCGATTGTTA-GGTCGG-A-A-TGCTGCTTATTTTGATAGATTGTTTA
1 TATGTTTAGATCGATTGTTATGGT-GGAATACTGCTGCTTATTTTGATAGATTGTGTA
* * * *
2282885 TATGTTTAAATCGATTGTTATGGTGGAATACTGCTTCTTCTTTTGAATTGATTGTGTA
1 TATGTTTAGATCGATTGTTATGGTGGAATACTGCTGCTTATTTTG-ATAGATTGTGTA
* **
2282943 TATGTTTAGATGGATTGTTATATTGGAATACTG
1 TATGTTTAGATCGATTGTTATGGTGGAATACTG
2282976 GTTGTTTTGA
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
54 21 0.27
55 4 0.05
56 1 0.01
57 12 0.16
58 39 0.51
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.47
Consensus pattern (57 bp):
TATGTTTAGATCGATTGTTATGGTGGAATACTGCTGCTTATTTTGATAGATTGTGTA
Found at i:2284643 original size:9 final size:9
Alignment explanation
Indices: 2284631--2284691 Score: 95
Period size: 9 Copynumber: 6.8 Consensus size: 9
2284621 TTTGGTTAAA
2284631 AATTAACCG
1 AATTAACCG
2284640 AATTAACCG
1 AATTAACCG
*
2284649 AATTACCCG
1 AATTAACCG
*
2284658 AATTACCCG
1 AATTAACCG
2284667 AATTAACCG
1 AATTAACCG
*
2284676 AATTACCCG
1 AATTAACCG
2284685 AATTAAC
1 AATTAAC
2284692 TAATTTGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 48 1.00
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:2284669 original size:27 final size:27
Alignment explanation
Indices: 2284631--2284691 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
2284621 TTTGGTTAAA
2284631 AATTAACCGAATTAACCGAATTACCCG
1 AATTAACCGAATTAACCGAATTACCCG
*
2284658 AATTACCCGAATTAACCGAATTACCCG
1 AATTAACCGAATTAACCGAATTACCCG
2284685 AATTAAC
1 AATTAAC
2284692 TAATTTGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (27 bp):
AATTAACCGAATTAACCGAATTACCCG
Found at i:2286865 original size:18 final size:19
Alignment explanation
Indices: 2286832--2286868 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2286822 AATAATTTTT
*
2286832 AAAATTTTAAATATTTATA
1 AAAATTCTAAATATTTATA
2286851 AAAATTCTAAA-ATTTATA
1 AAAATTCTAAATATTTATA
2286869 TTTTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATTCTAAATATTTATA
Found at i:2286873 original size:25 final size:27
Alignment explanation
Indices: 2286831--2286887 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 27
2286821 AAATAATTTT
* *
2286831 TAAAATTTTAAATATTTATAAAAATTC
1 TAAAATTTTAAATATTTAAAAAAATTA
*
2286858 TAAAA-TTTATAT-TTTAAAAAAATTA
1 TAAAATTTTAAATATTTAAAAAAATTA
2286883 TAAAA
1 TAAAA
2286888 ACTAAAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 16 0.59
26 6 0.22
27 5 0.19
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
TAAAATTTTAAATATTTAAAAAAATTA
Found at i:2291970 original size:27 final size:27
Alignment explanation
Indices: 2291932--2291991 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
2291922 GATATTTATA
*
2291932 TATGCTAAGAGAACATTGTAAAGTTCT
1 TATGCTAAGAGAACATTATAAAGTTCT
2291959 TATGCTAAGAGAACATTATAAAGTTCT
1 TATGCTAAGAGAACATTATAAAGTTCT
2291986 TATGCT
1 TATGCT
2291992 TGTTTAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (27 bp):
TATGCTAAGAGAACATTATAAAGTTCT
Found at i:2294685 original size:34 final size:35
Alignment explanation
Indices: 2294645--2294718 Score: 98
Period size: 34 Copynumber: 2.1 Consensus size: 35
2294635 AGCATATATT
* *
2294645 TATACTTATCAAT-TACATGTGCCGAATGCA-CATA
1 TATACTTAT-AATCCACATATGCCGAATGCAGCATA
2294679 TATACTTATAATCCACATATGCCGAATGCATGCATA
1 TATACTTATAATCCACATATGCCGAATGCA-GCATA
2294715 TATA
1 TATA
2294719 TATCCAACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 3 0.09
34 24 0.69
36 8 0.23
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.32
Consensus pattern (35 bp):
TATACTTATAATCCACATATGCCGAATGCAGCATA
Found at i:2294935 original size:41 final size:40
Alignment explanation
Indices: 2294890--2295122 Score: 315
Period size: 41 Copynumber: 5.7 Consensus size: 40
2294880 TTAAATAGAT
*
2294890 TCACCGGCACTTAGCCTGTTAGGCTTAAAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTAAA-CCTGATTCAGA
*
2294931 TCACCGACACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTA-AACCTGATTCAGA
* *
2294972 TCACCGGCACTTAGCCTGTTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTA-AACCTGATTCAGA
*
2295013 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGGTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTA-AACCTGATTCAGA
*
2295054 TCACCGGCACTTAGCCTGCTAGGTTTTAAAACCTGATTCAG-
1 TCACCGGCACTTAGCCTGCTAGG-CTT-AAACCTGATTCAGA
** *
2295095 TACACCGGCTTTTAGCCTGCTAGACTTA
1 T-CACCGGCACTTAGCCTGCTAGGCTTA
2295123 TAGTCCGAAA
Statistics
Matches: 174, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.01
41 138 0.79
42 34 0.20
43 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (40 bp):
TCACCGGCACTTAGCCTGCTAGGCTTAAACCTGATTCAGA
Found at i:2295027 original size:82 final size:82
Alignment explanation
Indices: 2294890--2295124 Score: 364
Period size: 82 Copynumber: 2.9 Consensus size: 82
2294880 TTAAATAGAT
*
2294890 TCACCGGCACTTAGCCTGTTAGGCTTAAAGCCTGATTCAGATCACCGACACTTAGCCTGCTAGGC
1 TCACCGGCACTTAGCCTGTTAGGCTTAAAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGC
2294955 TTATAACCTGATTCAGA
66 TTATAACCTGATTCAGA
*
2294972 TCACCGGCACTTAGCCTGTTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGC
1 TCACCGGCACTTAGCCTGTTAGGCTTAAAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGC
*
2295037 TTATAACCTGGTTCAGA
66 TTATAACCTGATTCAGA
* * * **
2295054 TCACCGGCACTTAGCCTGCTAGGTTTTAAAACCTGATTCAG-TACACCGGCTTTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGTTAGG-CTTAAAGCCTGATTCAGAT-CACCGGCACTTAGCCTGCTAG
*
2295118 ACTTATA
64 GCTTATA
2295125 GTCCGAAATG
Statistics
Matches: 141, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
82 102 0.72
83 39 0.28
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (82 bp):
TCACCGGCACTTAGCCTGTTAGGCTTAAAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGC
TTATAACCTGATTCAGA
Found at i:2295951 original size:72 final size:73
Alignment explanation
Indices: 2295825--2296075 Score: 344
Period size: 72 Copynumber: 3.3 Consensus size: 73
2295815 ACATTCAACA
2295825 TTAACTAAATTCAA-AACTTATTCATGTATATACACATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATG-ATAT----ATATATCCGAACTTTATATATATAAATAT
2295889 AACATACATACTT
61 AACATACATACTT
* *
2295902 TTAACTAAATTCAAGAATTTATTCATG-TATATATATCTGAACTTTATATATATAAATATAACAT
1 TTAACTAAATTCAAGAACTTATTCATGATATATATATCCGAACTTTATATATATAAATATAACAT
*
2295966 ACATAATT
66 ACATACTT
*
2295974 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATATCCGAACTTTATATATATAAAT
1 TTAACTAAATTCAAGAACTTATTCATG-------ATATATATATCCGAACTTTATATATATAAAT
2296039 ATAACATACATACTT
59 ATAACATACATACTT
2296054 TTAACTAAATTCAAGAACTTAT
1 TTAACTAAATTCAAGAACTTAT
2296076 ACATCTATAT
Statistics
Matches: 159, Mismatches: 6, Indels: 15
0.88 0.03 0.08
Matches are distributed among these distances:
72 67 0.42
76 3 0.02
77 14 0.09
78 11 0.07
80 64 0.40
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.39
Consensus pattern (73 bp):
TTAACTAAATTCAAGAACTTATTCATGATATATATATCCGAACTTTATATATATAAATATAACAT
ACATACTT
Found at i:2296114 original size:80 final size:78
Alignment explanation
Indices: 2295825--2296099 Score: 395
Period size: 80 Copynumber: 3.6 Consensus size: 78
2295815 ACATTCAACA
*
2295825 TTAACTAAATTCAA-AACTTATTCATGTATATACACATA-TATCCGAACTTTATATATATAAATA
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATTATCC-AACTTTATATATATAAATA
2295888 TAACATACATACTT
65 TAACATACATACTT
* * *
2295902 TTAACTAAATTCAAGAATTTATTCATG--TAT--ATATA-TCT-GAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATTATCCAACTTTATATATATAAATAT
*
2295961 AACATACATAATT
66 AACATACATACTT
*
2295974 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATATCCGAACTTTATATATATAAAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATAT-TATCC-AACTTTATATATATAAAT
2296039 ATAACATACATACTT
64 ATAACATACATACTT
* *
2296054 TTAACTAAATTCAAGAACTTATACATCTATATACATATATTATCCA
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATTATCCA
2296100 CTATTAGTTC
Statistics
Matches: 178, Mismatches: 11, Indels: 17
0.86 0.05 0.08
Matches are distributed among these distances:
72 59 0.33
74 9 0.05
76 8 0.04
77 14 0.08
78 14 0.08
79 5 0.03
80 69 0.39
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.39
Consensus pattern (78 bp):
TTAACTAAATTCAAGAACTTATTCATGTATATACATATATTATCCAACTTTATATATATAAATAT
AACATACATACTT
Found at i:2316231 original size:15 final size:17
Alignment explanation
Indices: 2316211--2316247 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2316201 ATATCAAAAA
2316211 ATAATA-TTAAA-AATC
1 ATAATACTTAAATAATC
*
2316226 ATAATACTTAAATAATT
1 ATAATACTTAAATAATC
2316243 ATAAT
1 ATAAT
2316248 TCCATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 5 0.26
17 8 0.42
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATACTTAAATAATC
Found at i:2318242 original size:18 final size:19
Alignment explanation
Indices: 2318199--2318244 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
2318189 ATGTCAAAAT
2318199 TTTATA-TTTAATTTATTA
1 TTTATATTTTAATTTATTA
*
2318217 TTTTTATTTTAATTTGA-TA
1 TTTATATTTTAATTT-ATTA
2318236 -TTATATTTT
1 TTTATATTTT
2318245 TATAATGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 13 0.54
19 10 0.42
20 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTATATTTTAATTTATTA
Found at i:2318242 original size:24 final size:25
Alignment explanation
Indices: 2318197--2318247 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
2318187 ATATGTCAAA
2318197 ATTTTATATTTAATTTATTATTTTT
1 ATTTTATATTTAATTTATTATTTTT
*
2318222 ATTTTA-ATTTGATATTA-TATTTTT
1 ATTTTATATTTAAT-TTATTATTTTT
2318246 AT
1 AT
2318248 AATGTTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (25 bp):
ATTTTATATTTAATTTATTATTTTT
Found at i:2322376 original size:33 final size:32
Alignment explanation
Indices: 2322325--2322484 Score: 96
Period size: 33 Copynumber: 4.8 Consensus size: 32
2322315 TTGTCTGTTA
*
2322325 TCGGTGGATTCAGCACTTAGCAACCACTAGTGAT
1 TCGG-GGAATCAGCACTTAGCAACCACTA-TGAT
*
2322359 TCGGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGAT
1 TCGGGGAATCAGCACTTAGCAA---C---CAC---TATGAT
* * * * *
2322400 ACGGTGGGATTAGCACTTAGCAACCACCAATGAG
1 TCGG-GGAATCAGCACTTAGCAACCA-CTATGAT
*
2322434 TCGGGGAATCAGCACTTAGCAACCCCT-TG--
1 TCGGGGAATCAGCACTTAGCAACCACTATGAT
2322463 --GGGGAATCAGCACTTAGCAACC
1 TCGGGGAATCAGCACTTAGCAACC
2322485 CCCTTCACAT
Statistics
Matches: 102, Mismatches: 13, Indels: 29
0.71 0.09 0.20
Matches are distributed among these distances:
27 22 0.22
31 2 0.02
32 1 0.01
33 35 0.34
34 10 0.10
36 3 0.03
37 1 0.01
39 4 0.04
41 6 0.06
42 18 0.18
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (32 bp):
TCGGGGAATCAGCACTTAGCAACCACTATGAT
Found at i:2322480 original size:102 final size:102
Alignment explanation
Indices: 2322361--2322561 Score: 339
Period size: 102 Copynumber: 2.0 Consensus size: 102
2322351 CTAGTGATTC
* * * *
2322361 GGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGGATTAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
*
2322426 CCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGAGTCGGGAAATCAGCACTTAGCAACCCCTTG
*
2322463 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCAGTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
*
2322528 CCAATGATTCGGGAAATCAGCACTTAGCAACCCC
66 CCAATGAGTCGGGAAATCAGCACTTAGCAACCCC
2322562 CTTTATATTC
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 92 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
CCAATGAGTCGGGAAATCAGCACTTAGCAACCCCTTG
Found at i:2333465 original size:20 final size:19
Alignment explanation
Indices: 2333440--2333480 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
2333430 AAATTAAGAG
2333440 TTATTT-TTTAATTTCATGTA
1 TTATTTATTT-ATTTCAT-TA
2333460 TTATTTATTTATTTCATTA
1 TTATTTATTTATTTCATTA
2333479 TT
1 TT
2333481 TTTCACATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 13 0.65
21 3 0.15
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.68
Consensus pattern (19 bp):
TTATTTATTTATTTCATTA
Found at i:2334212 original size:19 final size:18
Alignment explanation
Indices: 2334188--2334236 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
2334178 TAAAGGGTGA
2334188 GAAATAAAAGTTTTTGGGG
1 GAAATAAAAGTTTTT-GGG
2334207 GAAATAAAAAG-TTTTGGG
1 GAAAT-AAAAGTTTTTGGG
2334225 G-AATAAAAGTTT
1 GAAATAAAAGTTT
2334237 GAGGGAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.18
17 5 0.18
18 4 0.14
19 9 0.32
20 5 0.18
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.31
Consensus pattern (18 bp):
GAAATAAAAGTTTTTGGG
Found at i:2334367 original size:30 final size:31
Alignment explanation
Indices: 2334328--2334387 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
2334318 AGAGGTGGGA
*
2334328 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
2334359 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
2334388 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:2334495 original size:5 final size:5
Alignment explanation
Indices: 2334485--2334509 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2334475 TTGGGGGGTT
2334485 GGGAG GGGAG GGGAG GGGAG GGGAG
1 GGGAG GGGAG GGGAG GGGAG GGGAG
2334510 TAAAAGTTTT
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:0.20, C:0.00, G:0.80, T:0.00
Consensus pattern (5 bp):
GGGAG
Found at i:2336538 original size:46 final size:46
Alignment explanation
Indices: 2336482--2336574 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
2336472 TATAAGTGTA
* * *
2336482 TAGATATGGCTTAGTATTTGATATCAATGAAACTTTTATATATGTG
1 TAGATATGGCTTAATATTTAATATCAATAAAACTTTTATATATGTG
2336528 TAGATATGGCTTAATATTTAATATCAATAAAACTTTTATATATGTG
1 TAGATATGGCTTAATATTTAATATCAATAAAACTTTTATATATGTG
2336574 T
1 T
2336575 TGATGTGTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.44
Consensus pattern (46 bp):
TAGATATGGCTTAATATTTAATATCAATAAAACTTTTATATATGTG
Found at i:2337644 original size:5 final size:5
Alignment explanation
Indices: 2337636--2337684 Score: 98
Period size: 5 Copynumber: 9.8 Consensus size: 5
2337626 TCAAGTCAAG
2337636 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA TCGA
1 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA TCGA
2337685 GTGAAATTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (5 bp):
TCGAA
Found at i:2344534 original size:28 final size:26
Alignment explanation
Indices: 2344501--2344560 Score: 95
Period size: 25 Copynumber: 2.3 Consensus size: 26
2344491 AAAATTTATC
2344501 AAAATATTATAACTTTTTTTTATTTACG
1 AAAATATT-T-ACTTTTTTTTATTTACG
2344529 AAAATA-TTACTTTTTTTTATTTACG
1 AAAATATTTACTTTTTTTTATTTACG
2344554 AAAATAT
1 AAAATAT
2344561 ACCAAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
25 23 0.74
26 1 0.03
27 1 0.03
28 6 0.19
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (26 bp):
AAAATATTTACTTTTTTTTATTTACG
Found at i:2344546 original size:25 final size:25
Alignment explanation
Indices: 2344512--2344560 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
2344502 AAATATTATA
2344512 ACTTTTTTTTATTTACGAAAATATT
1 ACTTTTTTTTATTTACGAAAATATT
2344537 ACTTTTTTTTATTTACGAAAATAT
1 ACTTTTTTTTATTTACGAAAATAT
2344561 ACCAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.55
Consensus pattern (25 bp):
ACTTTTTTTTATTTACGAAAATATT
Found at i:2344698 original size:27 final size:27
Alignment explanation
Indices: 2344628--2344701 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
2344618 ACTGGGTCAG
* *
2344628 GCCAATGCCATTGGCAGCACCAATGGT
1 GCCAATACCATTGGCGGCACCAATGGT
*
2344655 GCCAATACCATTAGCGGCACCAATGGT
1 GCCAATACCATTGGCGGCACCAATGGT
*
2344682 GCC-ATACTGATTGGCGGCAC
1 GCCAATAC-CATTGGCGGCAC
2344702 TACTCGTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
26 4 0.10
27 37 0.90
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.19
Consensus pattern (27 bp):
GCCAATACCATTGGCGGCACCAATGGT
Found at i:2344943 original size:3 final size:3
Alignment explanation
Indices: 2344937--2344971 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2344927 AGTATTATTA
2344937 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
2344972 AGTATTAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:2348107 original size:11 final size:11
Alignment explanation
Indices: 2348091--2348117 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2348081 GCTTATGCTT
2348091 AAATTGTATCC
1 AAATTGTATCC
2348102 AAATTGTATCC
1 AAATTGTATCC
2348113 AAATT
1 AAATT
2348118 AAGTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (11 bp):
AAATTGTATCC
Found at i:2351207 original size:24 final size:25
Alignment explanation
Indices: 2351180--2351266 Score: 83
Period size: 26 Copynumber: 3.4 Consensus size: 25
2351170 ATGTACATAT
2351180 CATAACA-AAAATACGTATAATGTA
1 CATAACATAAAATACGTATAATGTA
2351204 CATAACATCAAAATA--TAT-ATGCTA
1 CATAACAT-AAAATACGTATAATG-TA
* *
2351228 AATAAAATATTAAAATACGTATAATGTA
1 CAT--AACA-TAAAATACGTATAATGTA
2351256 CATAACATAAA
1 CATAACATAAA
2351267 TTTTTAACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
23 3 0.06
24 14 0.28
25 4 0.08
26 18 0.36
27 1 0.02
28 7 0.14
29 3 0.06
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (25 bp):
CATAACATAAAATACGTATAATGTA
Found at i:2351361 original size:21 final size:21
Alignment explanation
Indices: 2351335--2351400 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
2351325 CCTTGCTTCC
2351335 CTCTTCTTCTTCTTTTTTTTT
1 CTCTTCTTCTTCTTTTTTTTT
* * *
2351356 CTCTTCTCCTTTCCTTTTCTTT
1 CTCTTCTTC-TTCTTTTTTTTT
*
2351378 C-CTTCTTTTTCTTTCTTTTTT
1 CTCTTCTTCTTCTTT-TTTTTT
2351399 CT
1 CT
2351401 TCTCCTTTCC
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 5 0.14
21 19 0.54
22 11 0.31
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (21 bp):
CTCTTCTTCTTCTTTTTTTTT
Found at i:2351362 original size:18 final size:17
Alignment explanation
Indices: 2351341--2351471 Score: 75
Period size: 18 Copynumber: 7.2 Consensus size: 17
2351331 TTCCCTCTTC
2351341 TTCTTCTTTTTTTTTCT
1 TTCTTCTTTTTTTTTCT
* **
2351358 CTTCTCCTTTCCTTTTCT
1 -TTCTTCTTTTTTTTTCT
*
2351376 TTCCTTCTTTTTCTTTCT
1 TT-CTTCTTTTTTTTTCT
*
2351394 TTTTTCTTCTCCTTTCCTCTTC-
1 TTCTTCTT-T--TTT--T-TTCT
*
2351416 TTCTTCTTTCTTTTTTTT
1 TTCTTCTTT-TTTTTTCT
* **
2351434 TTCTCCTTTCCTTTTCT
1 TTCTTCTTTTTTTTTCT
*
2351451 TTCCTTCTTTTTCTTTCT
1 TT-CTTCTTTTTTTTTCT
2351469 TTC
1 TTC
2351472 CTCTCCTTCC
Statistics
Matches: 85, Mismatches: 19, Indels: 19
0.69 0.15 0.15
Matches are distributed among these distances:
17 17 0.20
18 50 0.59
20 6 0.07
21 1 0.01
22 8 0.09
23 3 0.04
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (17 bp):
TTCTTCTTTTTTTTTCT
Found at i:2351383 original size:36 final size:36
Alignment explanation
Indices: 2351343--2351468 Score: 141
Period size: 41 Copynumber: 3.4 Consensus size: 36
2351333 CCCTCTTCTT
2351343 CTTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
* *
2351379 CTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTCTTC-TT-
1 CTTC---TT-TTT-TTTTCTCTTCTCCTTTCCTTTTCTTTC
*
2351418 CTTCTTTCTTTTTT-TTTTCTCCTTTCCTTTTCTTTC
1 CTTCTTT-TTTTTTCTCTTCTCCTTTCCTTTTCTTTC
*
2351454 CTTCTTTTTCTTTCT
1 CTTCTTTTTTTTTCT
2351469 TTCCTCTCCT
Statistics
Matches: 76, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
34 16 0.21
35 12 0.16
36 16 0.21
39 6 0.08
40 5 0.07
41 21 0.28
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (36 bp):
CTTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
Found at i:2351385 original size:13 final size:13
Alignment explanation
Indices: 2351369--2351506 Score: 71
Period size: 14 Copynumber: 10.8 Consensus size: 13
2351359 TTCTCCTTTC
2351369 CTTTTCTTTCCTT
1 CTTTTCTTTCCTT
2351382 CTTTTTCTTT-CTT
1 C-TTTTCTTTCCTT
2351395 -TTTTCTTCTCCTTT
1 CTTTTCTT-TCC-TT
*
2351409 CCTCTTC-TT-CTT
1 -CTTTTCTTTCCTT
2351421 C-TTTCTTT--TT
1 CTTTTCTTTCCTT
*
2351431 -TTTT-TCTCCTTT
1 CTTTTCTTTCC-TT
2351443 CCTTTTCTTTCCTT
1 -CTTTTCTTTCCTT
*
2351457 CTTTTTCTTTCTTT
1 C-TTTTCTTTCCTT
* * *
2351471 CCTCTCCTTCCTT
1 CTTTTCTTTCCTT
* *
2351484 CCTTTCTTTCTTT
1 CTTTTCTTTCCTT
2351497 C-TTTCTTTCC
1 CTTTTCTTTCC
2351507 CTCTCCTTCT
Statistics
Matches: 97, Mismatches: 13, Indels: 31
0.69 0.09 0.22
Matches are distributed among these distances:
9 2 0.02
10 8 0.08
11 10 0.10
12 13 0.13
13 26 0.27
14 29 0.30
15 5 0.05
16 4 0.04
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (13 bp):
CTTTTCTTTCCTT
Found at i:2351392 original size:4 final size:4
Alignment explanation
Indices: 2351371--2351505 Score: 72
Period size: 4 Copynumber: 34.0 Consensus size: 4
2351361 CTCCTTTCCT
*
2351371 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTC TTCTCC TTTCC TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C T-TTC
* * *
2351416 -TTC -TTC TTTC TTT- TTTT TTTC -TCC TTTCC TTTTC TTTC CTTC -TT-
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C -TTTC TTTC TTTC TTTC
* * *
2351460 TTTC TTTC TTTCC TCTCC TTCC TTCC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
2351506 CCTCTCCTTC
Statistics
Matches: 109, Mismatches: 7, Indels: 30
0.75 0.05 0.21
Matches are distributed among these distances:
3 22 0.20
4 66 0.61
5 12 0.11
6 9 0.08
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:2351430 original size:75 final size:75
Alignment explanation
Indices: 2351324--2351504 Score: 249
Period size: 75 Copynumber: 2.4 Consensus size: 75
2351314 TACCTTCTTT
* *
2351324 TCCTTGCTTCCCTCTTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTC
1 TCCTTCCTT-CCTCTTCTTCTTCTTTCTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTC
**
2351389 TTTCTTTTTTC
65 TTTCTTTCCTC
* * *
2351400 TTC-TCCTTTCCTCTTCTTCTTCTTTCTTTTTTTTTTCTCCTTTCCTTTTCTTTCCTTCTTTTTC
1 TCCTTCC-TTCCTCTTCTTCTTCTTTCTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTC
2351464 TTTCTTTCCTC
65 TTTCTTTCCTC
2351475 TCCTTCCTTCCT-TTCTTTCTTTCTTTCTTT
1 TCCTTCCTTCCTCTTC-TTC-TTCTTTCTTT
2351505 CCCTCTCCTT
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
74 3 0.03
75 73 0.78
76 17 0.18
ACGTcount: A:0.00, C:0.32, G:0.01, T:0.67
Consensus pattern (75 bp):
TCCTTCCTTCCTCTTCTTCTTCTTTCTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCT
TTCTTTCCTC
Found at i:2351454 original size:10 final size:9
Alignment explanation
Indices: 2351338--2351505 Score: 54
Period size: 10 Copynumber: 18.3 Consensus size: 9
2351328 TGCTTCCCTC
2351338 TTCTTCTTCT
1 TTCTT-TTCT
2351348 TT-TTTT-T
1 TTCTTTTCT
*
2351355 TCTCTTCTCCT
1 T-TCTT-TTCT
2351366 TTCCTTTTCT
1 TT-CTTTTCT
2351376 TTCCTTCTT-T
1 TT-CTT-TTCT
2351386 TTC-TTTC-
1 TTCTTTTCT
2351393 TT-TTTTCT
1 TTCTTTTCT
*
2351401 TCTCCTTTCCT
1 T-T-CTTTTCT
2351412 CTTCTTCTTCT
1 -TTCTT-TTCT
2351423 TTCTTTT-T
1 TTCTTTTCT
2351431 TT-TTTCTCCT
1 TTCTTT-T-CT
2351441 TTCCTTTTCT
1 TT-CTTTTCT
2351451 TTCCTTCTT-T
1 TT-CTT-TTCT
2351461 TTC-TTTCT
1 TTCTTTTCT
* * *
2351469 TTCCTCTCC
1 TTCTTTTCT
* *
2351478 TTCCTTCCT
1 TTCTTTTCT
2351487 TTC-TTTCT
1 TTCTTTTCT
2351495 TTC-TTTCT
1 TTCTTTTCT
2351503 TTC
1 TTC
2351506 CCTCTCCTTC
Statistics
Matches: 126, Mismatches: 10, Indels: 46
0.69 0.05 0.25
Matches are distributed among these distances:
7 15 0.12
8 29 0.23
9 21 0.17
10 38 0.30
11 19 0.15
12 4 0.03
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (9 bp):
TTCTTTTCT
Found at i:2351636 original size:10 final size:10
Alignment explanation
Indices: 2351621--2351660 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
2351611 CCTCGTTCGG
2351621 TGCAGCCTTT
1 TGCAGCCTTT
2351631 TGCAGCCTTT
1 TGCAGCCTTT
*
2351641 TGCAGGCTTT
1 TGCAGCCTTT
*
2351651 TTCAG-CTTT
1 TGCAGCCTTT
2351660 T
1 T
2351661 TTTTGTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
9 5 0.18
10 23 0.82
ACGTcount: A:0.10, C:0.25, G:0.20, T:0.45
Consensus pattern (10 bp):
TGCAGCCTTT
Found at i:2351703 original size:23 final size:24
Alignment explanation
Indices: 2351677--2351738 Score: 99
Period size: 23 Copynumber: 2.6 Consensus size: 24
2351667 TTGTTTTGGT
2351677 ATATTTTGGTAATTAAAAAA-ATA
1 ATATTTTGGTAATTAAAAAAGATA
*
2351700 ATATTTTGGTAAATAAAAAAGGATA
1 ATATTTTGGTAATTAAAAAA-GATA
2351725 ATATTTTGGTAATT
1 ATATTTTGGTAATT
2351739 TTAATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 19 0.54
25 16 0.46
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (24 bp):
ATATTTTGGTAATTAAAAAAGATA
Found at i:2357844 original size:34 final size:34
Alignment explanation
Indices: 2357805--2357877 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
2357795 CAAATGATAG
2357805 TGTTAATTATTTCCATTAATACATGACATGTATA
1 TGTTAATTATTTCCATTAATACATGACATGTATA
2357839 TGTTAATTATTTCCATTAATACATGACATGTATA
1 TGTTAATTATTTCCATTAATACATGACATGTATA
2357873 TGTTA
1 TGTTA
2357878 TAAACTAGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (34 bp):
TGTTAATTATTTCCATTAATACATGACATGTATA
Found at i:2362197 original size:28 final size:28
Alignment explanation
Indices: 2362157--2362234 Score: 138
Period size: 28 Copynumber: 2.8 Consensus size: 28
2362147 CTCACTCATT
*
2362157 TGTTAGAAAGAGTACGGAATCTAAGGAA
1 TGTTAGAAAGAGTACAGAATCTAAGGAA
2362185 TGTTAGAAAGAGTACAGAATCTAAGGAA
1 TGTTAGAAAGAGTACAGAATCTAAGGAA
*
2362213 TGTTAGAAAGAGTACACAATCT
1 TGTTAGAAAGAGTACAGAATCT
2362235 GTAAATAGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.23
Consensus pattern (28 bp):
TGTTAGAAAGAGTACAGAATCTAAGGAA
Found at i:2362468 original size:138 final size:138
Alignment explanation
Indices: 2362220--2362635 Score: 814
Period size: 138 Copynumber: 3.0 Consensus size: 138
2362210 GAATGTTAGA
2362220 AAGAGTACACAATCTGTAAATAGATACAATTTCTGCTCTGCTATGGTTTCTATCCTTGCAGCTAA
1 AAGAGTACACAATCTGTAAATAGATACAATTTCTGCTCTGCTATGGTTTCTATCCTTGCAGCTAA
2362285 AAAGGATAACTTTTAGTTATTTCCCTCTCACATTTCTAAAGTTAACGTTTTCATCACTTATTTTT
66 AAAGGATAACTTTTAGTTATTTCCCTCTCACATTTCTAAAGTTAACGTTTTCATCACTTATTTTT
2362350 GTCAAGTT
131 GTCAAGTT
2362358 AAGAGTACACAATCTGTAAATAGATACAATTTCTGCTCTGCTATGGTTTCTATCCTTGCAGCTAA
1 AAGAGTACACAATCTGTAAATAGATACAATTTCTGCTCTGCTATGGTTTCTATCCTTGCAGCTAA
2362423 AAAGGATAACTTTTAGTTATTTCCCTCTCACATTTCTAAAGTTAACGTTTTCATCACTTATTTTT
66 AAAGGATAACTTTTAGTTATTTCCCTCTCACATTTCTAAAGTTAACGTTTTCATCACTTATTTTT
2362488 GTCAAGTT
131 GTCAAGTT
2362496 AAGAGTACACAATCTGTAAATAGATACAATTTCTGCTCTGCTATGGTTTCTATCCTTGCAGCTAA
1 AAGAGTACACAATCTGTAAATAGATACAATTTCTGCTCTGCTATGGTTTCTATCCTTGCAGCTAA
* *
2362561 AAAGGATAACTTTTAGTTATTTCCCTCTCACATTTCTAAAATTTACGTTTTCATCACTTATTTTT
66 AAAGGATAACTTTTAGTTATTTCCCTCTCACATTTCTAAAGTTAACGTTTTCATCACTTATTTTT
2362626 GTCAAGTT
131 GTCAAGTT
2362634 AA
1 AA
2362636 CGTTTTCATC
Statistics
Matches: 276, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 276 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (138 bp):
AAGAGTACACAATCTGTAAATAGATACAATTTCTGCTCTGCTATGGTTTCTATCCTTGCAGCTAA
AAAGGATAACTTTTAGTTATTTCCCTCTCACATTTCTAAAGTTAACGTTTTCATCACTTATTTTT
GTCAAGTT
Found at i:2364432 original size:78 final size:78
Alignment explanation
Indices: 2364343--2364504 Score: 288
Period size: 78 Copynumber: 2.1 Consensus size: 78
2364333 ATGTGTGATC
* * *
2364343 TTAAATTATCATATCTTTTGCTAATTTATTACAATTTTTCAATAAAAATATATTTAAATGACAAA
1 TTAAATCATCATATCTTTTGCTAATCTATTACAATTTTTCAATAAAAATATATCTAAATGACAAA
2364408 TACTTAATATAAT
66 TACTTAATATAAT
2364421 TTAAATCATCATATCTTTTGCTAATCTATTACAATTTTTCAATAAAAATATATCTAAATGACAAA
1 TTAAATCATCATATCTTTTGCTAATCTATTACAATTTTTCAATAAAAATATATCTAAATGACAAA
2364486 TACTTAATATAAT
66 TACTTAATATAAT
*
2364499 TAAAAT
1 TTAAAT
2364505 TAAAAATTGT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.43
Consensus pattern (78 bp):
TTAAATCATCATATCTTTTGCTAATCTATTACAATTTTTCAATAAAAATATATCTAAATGACAAA
TACTTAATATAAT
Found at i:2365832 original size:19 final size:20
Alignment explanation
Indices: 2365805--2365843 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2365795 AAAAAATTAA
2365805 TATTATTTTG-ATATTTTTT
1 TATTATTTTGAATATTTTTT
*
2365824 TATTTTTTTGTAATATTTTT
1 TATTATTTTG-AATATTTTT
2365844 ATAAAAGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
21 8 0.47
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (20 bp):
TATTATTTTGAATATTTTTT
Found at i:2370978 original size:23 final size:21
Alignment explanation
Indices: 2370952--2370996 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
2370942 AAATTGAAGG
*
2370952 ACCAAACTCTAATAAATTTTTAT
1 ACCAAA-TCT-ATAAATATTTAT
*
2370975 ACCAAATCTGTAAATATTTAT
1 ACCAAATCTATAAATATTTAT
2370996 A
1 A
2370997 TTTAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 3 0.15
23 6 0.30
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (21 bp):
ACCAAATCTATAAATATTTAT
Found at i:2371121 original size:48 final size:48
Alignment explanation
Indices: 2371045--2371140 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
2371035 CAAAACCACC
2371045 TTTCCTGATACCACTAGAAATCGAGTTGTTACAACGATAACTTTTCTT
1 TTTCCTGATACCACTAGAAATCGAGTTGTTACAACGATAACTTTTCTT
*
2371093 TTTCCTGATACCACTAGAAATCGGGTTGTTACAACGATAACTTTTCTT
1 TTTCCTGATACCACTAGAAATCGAGTTGTTACAACGATAACTTTTCTT
2371141 ATCAAGTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (48 bp):
TTTCCTGATACCACTAGAAATCGAGTTGTTACAACGATAACTTTTCTT
Found at i:2372511 original size:19 final size:19
Alignment explanation
Indices: 2372436--2372512 Score: 50
Period size: 19 Copynumber: 3.8 Consensus size: 19
2372426 TAAATTAGTT
2372436 AATTAAAATATGTTTTAAAAA
1 AATTAAAAT-TG-TTTAAAAA
* *
2372457 AATTATAA-CG-TTAATATTAA
1 AATTAAAATTGTTTAA-A--AA
* *
2372477 AATTTAAAAATATTTAAAAA
1 AA-TTAAAATTGTTTAAAAA
2372497 AATTAAAATTGTTTAA
1 AATTAAAATTGTTTAA
2372513 TTTTCAATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 14
0.67 0.11 0.22
Matches are distributed among these distances:
17 4 0.09
18 1 0.02
19 13 0.30
20 8 0.19
21 12 0.28
22 1 0.02
23 4 0.09
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (19 bp):
AATTAAAATTGTTTAAAAA
Found at i:2377554 original size:24 final size:24
Alignment explanation
Indices: 2377525--2377573 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2377515 GGTAAACAAA
* *
2377525 TTGAAGCTAGAAGTTGAAATGATG
1 TTGAAGCTAGAAGCTGAAATAATG
*
2377549 TTGAAGCTTGAAGCTGAAATAATG
1 TTGAAGCTAGAAGCTGAAATAATG
2377573 T
1 T
2377574 AGCTGTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.31
Consensus pattern (24 bp):
TTGAAGCTAGAAGCTGAAATAATG
Found at i:2379241 original size:280 final size:282
Alignment explanation
Indices: 2378737--2379250 Score: 987
Period size: 280 Copynumber: 1.8 Consensus size: 282
2378727 TATAGGAATT
*
2378737 TTCTTGTCTCTTCATAGAGACATCTTTCAATAGGTGTCTTTATGAATAAATAAATAATAATAATT
1 TTCTTGTCTCTTCATAGAGACATCTTTCAATAGATGTCTTTATGAATAAAT-AATAATAATAATT
2378802 ATTCATTTAATTTTGTAACTATTCAAATAATATTTTTTGAATAATTATAATTCTTTTTAAAAAAA
65 ATTCATTTAATTTTGTAACTATTCAAATAATATTTTTTGAATAATTATAATTCTTTTTAAAAAAA
2378867 TCAAATGATATAACTTTTGACCAATGACCAAAAGATTTATCTTTTGATTAATTACACCCATTCAT
130 TCAAATGATATAACTTTTGACCAATGACCAAAAGATTTATCTTTTGATTAATTACACCCATTCAT
2378932 TTATAGTTATTGGGATACTATAAATATTTGAAAATGTTCCAACAATCTCCCCCCATTTTCAAAAT
195 TTATAGTTATTGGGATACTATAAATATTTGAAAATGTTCCAACAATCTCCCCCCATTTTCAAAAT
2378997 ATTTAGATTTTGATATTCTTGGC
260 ATTTAGATTTTGATATTCTTGGC
*
2379020 TTCTTGTCTCTTCATAGATACATCTTTCAATAGATGTCTTTATGAATAAAT-A-AATAATAATTA
1 TTCTTGTCTCTTCATAGAGACATCTTTCAATAGATGTCTTTATGAATAAATAATAATAATAATTA
2379083 TTCATTTAATTTTGTAACTATTCAAATAATATTTTTTGAATAATTATAATTCTTTTTAAAAAAAT
66 TTCATTTAATTTTGTAACTATTCAAATAATATTTTTTGAATAATTATAATTCTTTTTAAAAAAAT
2379148 CAAATGATATAACTTTTGACCAATGACCAAAAGATTTATCTTTTGATTAATTACACCCATTCATT
131 CAAATGATATAACTTTTGACCAATGACCAAAAGATTTATCTTTTGATTAATTACACCCATTCATT
2379213 TATAGTTATTGGGATACTATAAATATTTGAAAATGTTC
196 TATAGTTATTGGGATACTATAAATATTTGAAAATGTTC
2379251 TAACCAGAAA
Statistics
Matches: 229, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
280 179 0.78
281 1 0.00
283 49 0.21
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (282 bp):
TTCTTGTCTCTTCATAGAGACATCTTTCAATAGATGTCTTTATGAATAAATAATAATAATAATTA
TTCATTTAATTTTGTAACTATTCAAATAATATTTTTTGAATAATTATAATTCTTTTTAAAAAAAT
CAAATGATATAACTTTTGACCAATGACCAAAAGATTTATCTTTTGATTAATTACACCCATTCATT
TATAGTTATTGGGATACTATAAATATTTGAAAATGTTCCAACAATCTCCCCCCATTTTCAAAATA
TTTAGATTTTGATATTCTTGGC
Found at i:2380630 original size:299 final size:301
Alignment explanation
Indices: 2380090--2380673 Score: 852
Period size: 299 Copynumber: 1.9 Consensus size: 301
2380080 ATAGGCCTTC
2380090 TCCAAATCTATCTTAATAACCATCCATATTTTGTGTTTGCTTCTCATGGAATAAATAACTTCTTG
1 TCCAAATCTATCTTAATAACCATCCATATTTTGTGTTTGCTTCTCATGGAATAAATAACTTCTTG
* * * *
2380155 GACGACTATGATATTGTTAGTGATGTTCCTTCCAGCAAAAAAACCCACCTATTCTAGGTCAATGA
66 GACGACTATGATATTGTTAGTGATATTACTTCCAGCAAAAAAACCCACATATTCTAGGCCAATGA
* * * * * *
2380220 TTCTAGGAAAAACAACCTTATATTTGTTCGGAATGGTATTTATGACTTGCATGTAAAGAACTGAA
131 TTCTAGGAAAAACAACCTTATATCTATTCAGAATGATATTTAGGACCTGCATGTAAAGAACTGAA
* * *
2380285 CACAAGTTTATTGGGCGAAATTGTGCAAAGTTTGTGCAATTAAAGGGTAAAAGGGATATATTAGA
196 CACAAATTTATTGGGCGAAATTGTGCAAAGTTTGTGCAATTAAAGGGTAAAAGGGATATATCAAA
2380350 GGGTACTTTATTGTCATGGAATTAAGAGGCATAATAGCTTA
261 GGGTACTTTATTGTCATGGAATTAAGAGGCATAATAGCTTA
* ** * *
2380391 TCCAAATCTATCTTGATGGCCATCCATCTTTTGTGTTTGC-TCTCATGG-ATGAATAACTTCTTG
1 TCCAAATCTATCTTAATAACCATCCATATTTTGTGTTTGCTTCTCATGGAATAAATAACTTCTTG
** * * * * *
2380454 GGTGATTATGATATTGTTAGTGATATTACTTCCAG-AAATAAAACCCGCATTTTCTGGGCCAGTG
66 GACGACTATGATATTGTTAGTGATATTACTTCCAGCAAA-AAAACCCACATATTCTAGGCCAATG
* *
2380518 ATTCTAGGAAAAACAACCTTATATCTATTCAGAATGATCTTTAGGACCTGCTTGTAAAGAACTGA
130 ATTCTAGGAAAAACAACCTTATATCTATTCAGAATGATATTTAGGACCTGCATGTAAAGAACTGA
* *
2380583 ACACAAATTTATTGGGTGAAATTGTGCAAAGTTCT-TGCAATTAAAGGGTAGAAGGGATATATCA
195 ACACAAATTTATTGGGCGAAATTGTGCAAAGTT-TGTGCAATTAAAGGGTAAAAGGGATATATCA
*
2380647 AAGGGTATTTTATTGTCATGGAATTAA
259 AAGGGTACTTTATTGTCATGGAATTAA
2380674 AAGGTAGAAT
Statistics
Matches: 251, Mismatches: 30, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
298 3 0.01
299 203 0.81
300 9 0.04
301 36 0.14
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (301 bp):
TCCAAATCTATCTTAATAACCATCCATATTTTGTGTTTGCTTCTCATGGAATAAATAACTTCTTG
GACGACTATGATATTGTTAGTGATATTACTTCCAGCAAAAAAACCCACATATTCTAGGCCAATGA
TTCTAGGAAAAACAACCTTATATCTATTCAGAATGATATTTAGGACCTGCATGTAAAGAACTGAA
CACAAATTTATTGGGCGAAATTGTGCAAAGTTTGTGCAATTAAAGGGTAAAAGGGATATATCAAA
GGGTACTTTATTGTCATGGAATTAAGAGGCATAATAGCTTA
Found at i:2381083 original size:25 final size:25
Alignment explanation
Indices: 2381043--2381091 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2381033 TGCACACCAA
* *
2381043 ACAATTTTTCTTTATCATTTTTTTT
1 ACAATTTCTCTCTATCATTTTTTTT
2381068 ACAATTTCTCTCTATCATTTTTTT
1 ACAATTTCTCTCTATCATTTTTTT
2381092 GTACCCTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.63
Consensus pattern (25 bp):
ACAATTTCTCTCTATCATTTTTTTT
Found at i:2383729 original size:33 final size:33
Alignment explanation
Indices: 2383691--2383758 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
2383681 AGGGTGTTTT
* * * *
2383691 GATGACTTTTGGATGCCAAAATTGCCCCTACAC
1 GATGACTTTTCGATACCAAAAATGCCCATACAC
2383724 GATGACTTTTCGATACCAAAAATGCCCATACAC
1 GATGACTTTTCGATACCAAAAATGCCCATACAC
2383757 GA
1 GA
2383759 GCCTTGTGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.25
Consensus pattern (33 bp):
GATGACTTTTCGATACCAAAAATGCCCATACAC
Found at i:2385519 original size:50 final size:51
Alignment explanation
Indices: 2385406--2385531 Score: 173
Period size: 50 Copynumber: 2.5 Consensus size: 51
2385396 ACATGTCAAA
* ** * *
2385406 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACAGGGGATCCTCTCATCTCGGTGCCAAT
* * *
2385457 GCCATGTCCCAGACATGATCTTACGGGGGA-CCTCTCGTCTCGGTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACAGGGGATCCTCTCATCTCGGTGCCAAT
2385507 GCCATGTCCCAGACATGGTCTTACA
1 GCCATGTCCCAGACATGGTCTTACA
2385532 CGATGCCAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 38 0.58
51 27 0.42
ACGTcount: A:0.19, C:0.30, G:0.25, T:0.26
Consensus pattern (51 bp):
GCCATGTCCCAGACATGGTCTTACAGGGGATCCTCTCATCTCGGTGCCAAT
Found at i:2385546 original size:35 final size:35
Alignment explanation
Indices: 2385500--2385566 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
2385490 CTCGTCTCGG
2385500 TGCCAATGCCATGTCCCAGACATGGTCTTACACGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACACGA
* **
2385535 TGCCAATGCCATGTTCCAGTTATGGTCTTACA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA
2385567 TGAGAGCTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (35 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACACGA
Found at i:2385998 original size:30 final size:30
Alignment explanation
Indices: 2385964--2386020 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2385954 CCTCGACTCT
2385964 AACTTTGTA-AAAATTACAATTTTGCCCCTA
1 AACTTT-TACAAAATTACAATTTTGCCCCTA
* *
2385994 AACTTTTACATAATTACATTTTTGCCC
1 AACTTTTACAAAATTACAATTTTGCCC
2386021 TAAGGCTCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.40
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:2388714 original size:3 final size:3
Alignment explanation
Indices: 2388699--2388751 Score: 97
Period size: 3 Copynumber: 17.3 Consensus size: 3
2388689 ACAAATATAT
2388699 TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2388745 TAA TAA T
1 TAA TAA T
2388752 GATAGTACTA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2389563 original size:16 final size:16
Alignment explanation
Indices: 2389542--2389572 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2389532 TTTATACTGA
*
2389542 AAATAATCATAATAAT
1 AAATAATAATAATAAT
2389558 AAATAATAATAATAA
1 AAATAATAATAATAA
2389573 ATCCTATATC
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:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAATAATAATAAT
Found at i:2389568 original size:13 final size:13
Alignment explanation
Indices: 2389550--2389574 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2389540 GAAAATAATC
2389550 ATAATAATAAATA
1 ATAATAATAAATA
2389563 ATAATAATAAAT
1 ATAATAATAAAT
2389575 CCTATATCTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAATAATAAATA
Found at i:2389697 original size:36 final size:36
Alignment explanation
Indices: 2389650--2389730 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
2389640 AGGGCGACTT
*
2389650 GCTGCAACGTTCGCGGAGTTGCTGTGCATGGGTGAG
1 GCTGCTACGTTCGCGGAGTTGCTGTGCATGGGTGAG
*
2389686 GCTGCTACGTTCGCGGAGTTGCTGTGCGTGGGTGAG
1 GCTGCTACGTTCGCGGAGTTGCTGTGCATGGGTGAG
2389722 GCTGCTACG
1 GCTGCTACG
2389731 ACAGAGGCGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.11, C:0.21, G:0.42, T:0.26
Consensus pattern (36 bp):
GCTGCTACGTTCGCGGAGTTGCTGTGCATGGGTGAG
Found at i:2392002 original size:21 final size:22
Alignment explanation
Indices: 2391976--2392024 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
2391966 AAAATTTTTT
2391976 TAAAAAATTAAATTAAAAA-AA
1 TAAAAAATTAAATTAAAAAGAA
* * *
2391997 TAAAAAATTTATTTAAAAAGTA
1 TAAAAAATTAAATTAAAAAGAA
2392019 TAAAAA
1 TAAAAA
2392025 TTATAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
TAAAAAATTAAATTAAAAAGAA
Found at i:2392034 original size:20 final size:19
Alignment explanation
Indices: 2391989--2392037 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
2391979 AAAATTAAAT
2391989 TAAAAAAATAAAAAATTTA
1 TAAAAAAATAAAAAATTTA
* *
2392008 TTTAAAAAGTATAAAAA-TTA
1 -TAAAAAAATA-AAAAATTTA
2392028 TAAAAAAATA
1 TAAAAAAATA
2392038 TTTTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 8 0.33
20 11 0.46
21 5 0.21
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
TAAAAAAATAAAAAATTTA
Found at i:2392046 original size:12 final size:12
Alignment explanation
Indices: 2392031--2392056 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2392021 AAAATTATAA
2392031 AAAAATATTTTT
1 AAAAATATTTTT
2392043 AAAAATATTTTT
1 AAAAATATTTTT
2392055 AA
1 AA
2392057 TTTAAAAAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AAAAATATTTTT
Found at i:2395901 original size:51 final size:51
Alignment explanation
Indices: 2395842--2395939 Score: 169
Period size: 51 Copynumber: 1.9 Consensus size: 51
2395832 GTTTAGGGCC
* **
2395842 AATTGGGCCGAATTAGAATCCTTGGTAAATAGTGAAGCATGCGCGGAGATA
1 AATTGGGCCGAATTAGAATCCTTAGTAAATAAAGAAGCATGCGCGGAGATA
2395893 AATTGGGCCGAATTAGAATCCTTAGTAAATAAAGAAGCATGCGCGGA
1 AATTGGGCCGAATTAGAATCCTTAGTAAATAAAGAAGCATGCGCGGA
2395940 AATATATTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (51 bp):
AATTGGGCCGAATTAGAATCCTTAGTAAATAAAGAAGCATGCGCGGAGATA
Found at i:2399656 original size:21 final size:21
Alignment explanation
Indices: 2399630--2399670 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2399620 AGACGAGCAA
* *
2399630 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2399651 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2399671 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:2401609 original size:16 final size:16
Alignment explanation
Indices: 2401576--2401609 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2401566 GGAGATTGTT
* *
2401576 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
2401592 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
2401608 AA
1 AA
2401610 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:2407895 original size:24 final size:24
Alignment explanation
Indices: 2407863--2407911 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2407853 ATAATGCCTT
2407863 AAACTCGTATTCTTAATTCGTTAA
1 AAACTCGTATTCTTAATTCGTTAA
2407887 AAACTCGTATTCTTAATTCGTTAA
1 AAACTCGTATTCTTAATTCGTTAA
2407911 A
1 A
2407912 CTGATGAATA
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:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (24 bp):
AAACTCGTATTCTTAATTCGTTAA
Found at i:2415161 original size:12 final size:11
Alignment explanation
Indices: 2415139--2415168 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
2415129 TAAAATTAGT
2415139 TAAATAATAAA
1 TAAATAATAAA
2415150 TAAATGAATAAA
1 TAAAT-AATAAA
2415162 TAAATAA
1 TAAATAA
2415169 AAAGGATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (11 bp):
TAAATAATAAA
Found at i:2424051 original size:39 final size:39
Alignment explanation
Indices: 2424008--2424865 Score: 1716
Period size: 39 Copynumber: 22.0 Consensus size: 39
2423998 GAGAAATTTG
2424008 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424047 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424086 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424125 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424164 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424203 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424242 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424281 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424320 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424359 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424398 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424437 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424476 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424515 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424554 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424593 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424632 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424671 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424710 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424749 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424788 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424827 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
1 ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
2424866 CATAATGATA
Statistics
Matches: 819, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 819 1.00
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.51
Consensus pattern (39 bp):
ATGTGTATGTATGATACTATTATCATTTTCTTAAGTTTA
Done.