Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 7 of 216
Found at i:2320577 original size:18 final size:18
Alignment explanation
Indices: 2320528--2320578 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
2320518 AAACAAAAGA
2320528 AGAACAGAAAAG-AAACAG
1 AGAA-AGAAAAGAAAACAG
* *
2320546 AGAAAGAGACGAAAACAG
1 AGAAAGAAAAGAAAACAG
* *
2320564 GGGAAGAAAAGAAAA
1 AGAAAGAAAAGAAAA
2320579 GGGGAAAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
17 5 0.19
18 21 0.81
ACGTcount: A:0.65, C:0.08, G:0.27, T:0.00
Consensus pattern (18 bp):
AGAAAGAAAAGAAAACAG
Found at i:2320933 original size:22 final size:24
Alignment explanation
Indices: 2320907--2320950 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
2320897 TATAGCATGA
2320907 AATTAAG-TAGAAAAG-AAGTATG
1 AATTAAGTTAGAAAAGTAAGTATG
2320929 AATTAAGTTAGAAAAGTAAGTA
1 AATTAAGTTAGAAAAGTAAGTA
2320951 AGCTTAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (24 bp):
AATTAAGTTAGAAAAGTAAGTATG
Found at i:2323846 original size:5 final size:5
Alignment explanation
Indices: 2323836--2323912 Score: 65
Period size: 5 Copynumber: 15.6 Consensus size: 5
2323826 AAAAAAATAT
* *
2323836 TATTA TATTA TAGTAA TGATTA TGTT- T-TTA TATTA TATTA TTATTA
1 TATTA TATTA TA-TTA T-ATTA TATTA TATTA TATTA TATTA -TATTA
2323882 -A-TA TATTA TATTA TATTA TA-TA TATATA TAT
1 TATTA TATTA TATTA TATTA TATTA TAT-TA TAT
2323913 AGCAAAAGAA
Statistics
Matches: 60, Mismatches: 3, Indels: 17
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.13
5 31 0.52
6 16 0.27
7 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:2323888 original size:19 final size:19
Alignment explanation
Indices: 2323864--2323912 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 19
2323854 ATTATGTTTT
2323864 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
2323883 TATATTATATTATATTATA
1 TATATTATATTATATTATA
2323902 TATATATATAT
1 TATAT-TATAT
2323913 AGCAAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.18
19 18 0.64
20 5 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:2325311 original size:25 final size:24
Alignment explanation
Indices: 2325244--2325375 Score: 180
Period size: 25 Copynumber: 5.5 Consensus size: 24
2325234 ACTTTAGCGC
2325244 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
2325268 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
2325292 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGA-TATTAGCACGTTGGT
***
2325317 GCTCTCTGATATTTAGCACGGCAGT
1 GCTCTCTGATA-TTAGCACGTTGGT
* *
2325342 GCTCTCTG-T-TTAGCACATTTGT
1 GCTCTCTGATATTAGCACGTTGGT
2325364 GCTCTCTG-TATT
1 GCTCTCTGATATT
2325376 TGTTCCGTAT
Statistics
Matches: 98, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
22 18 0.18
23 2 0.02
24 36 0.37
25 42 0.43
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (24 bp):
GCTCTCTGATATTAGCACGTTGGT
Found at i:2325311 original size:49 final size:48
Alignment explanation
Indices: 2325244--2325375 Score: 180
Period size: 49 Copynumber: 2.8 Consensus size: 48
2325234 ACTTTAGCGC
***
2325244 GCTCTCTGATATTAGCACGTTGGTGCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGTGCTCTCTGATATTAGCACGGCAGT
2325292 GCTCTCTGATTATTAGCACGTTGGTGCTCTCTGATATTTAGCACGGCAGT
1 GCTCTCTGA-TATTAGCACGTTGGTGCTCTCTGATA-TTAGCACGGCAGT
* *
2325342 GCTCTCTG-T-TTAGCACATTTGTGCTCTCTG-TATT
1 GCTCTCTGATATTAGCACGTTGGTGCTCTCTGATATT
2325376 TGTTCCGTAT
Statistics
Matches: 77, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
45 2 0.03
46 2 0.03
47 19 0.25
48 10 0.13
49 26 0.34
50 18 0.23
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (48 bp):
GCTCTCTGATATTAGCACGTTGGTGCTCTCTGATATTAGCACGGCAGT
Found at i:2326207 original size:17 final size:17
Alignment explanation
Indices: 2326185--2326218 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2326175 ATGTGGCATG
*
2326185 TACCTAGGTAATGTATA
1 TACCTAAGTAATGTATA
*
2326202 TACCTAAGTGATGTATA
1 TACCTAAGTAATGTATA
2326219 GGGATTAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
TACCTAAGTAATGTATA
Found at i:2332562 original size:22 final size:20
Alignment explanation
Indices: 2332512--2332563 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 20
2332502 GAGAGCTTTC
*
2332512 AATCAAAAAAAAGTAAAAAG
1 AATCAAAAAAAAGAAAAAAG
2332532 AAGTCCAAAAAAACAGAAAAAAG
1 AA-T-CAAAAAAA-AGAAAAAAG
2332555 TAATCAAAA
1 -AATCAAAA
2332564 CTCAAAAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.07
21 1 0.04
22 13 0.48
23 9 0.33
24 2 0.07
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (20 bp):
AATCAAAAAAAAGAAAAAAG
Found at i:2347904 original size:18 final size:18
Alignment explanation
Indices: 2347881--2347973 Score: 141
Period size: 18 Copynumber: 5.2 Consensus size: 18
2347871 TACGATTATT
2347881 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
2347899 TACGGTACTATTCATGTA
1 TACGGTACTATTCACGTA
*
2347917 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
2347935 TATGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
2347953 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
2347971 TAC
1 TAC
2347974 AGTAGTTGGG
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:2353775 original size:15 final size:16
Alignment explanation
Indices: 2353749--2353779 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2353739 GGGTCACGGG
2353749 TCAGGTGCCAAAACGA
1 TCAGGTGCCAAAACGA
2353765 TCAGG-GCCAAAACGA
1 TCAGGTGCCAAAACGA
2353780 CGTCGTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.39, C:0.26, G:0.26, T:0.10
Consensus pattern (16 bp):
TCAGGTGCCAAAACGA
Found at i:2358970 original size:28 final size:28
Alignment explanation
Indices: 2358910--2358963 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
2358900 CAGTAACAGT
* * * *
2358910 ACAGTGTGGGCCTTAGCCCTATACAAAA
1 ACAGTGTAGGCCTAAGCCCGACACAAAA
2358938 ACAGTGTAGGCCTAAGCCCGACACAA
1 ACAGTGTAGGCCTAAGCCCGACACAA
2358964 TATCAGTATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.17
Consensus pattern (28 bp):
ACAGTGTAGGCCTAAGCCCGACACAAAA
Found at i:2359131 original size:26 final size:26
Alignment explanation
Indices: 2359079--2359131 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
2359069 CACTAATATC
* *
2359079 GCAGCATAGCTGCCAGTAGTAATAAT
1 GCAGCAGAGCTGCCAGTAGTAAGAAT
*
2359105 GCAGCAGAGCTGCCAGTAGTCAGAAT
1 GCAGCAGAGCTGCCAGTAGTAAGAAT
2359131 G
1 G
2359132 GCTAAAAGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.19
Consensus pattern (26 bp):
GCAGCAGAGCTGCCAGTAGTAAGAAT
Found at i:2359276 original size:32 final size:32
Alignment explanation
Indices: 2359175--2359329 Score: 139
Period size: 32 Copynumber: 4.8 Consensus size: 32
2359165 TAAACAGAAT
* * * *
2359175 GGTAATATGATTGGCACAAAGCCATCAGTAGC
1 GGTAATATGATCGACACAAAGCCATCAATAAC
* ** ** * ** *
2359207 AGTGTTATGATCGGTACACAGTAATCAGTAAC
1 GGTAATATGATCGACACAAAGCCATCAATAAC
* ** *
2359239 TGTAATATGATCGACACAAAGCCATCGGTAAT
1 GGTAATATGATCGACACAAAGCCATCAATAAC
2359271 GGTAATATGATCGACACAAAGCCATCAATAAC
1 GGTAATATGATCGACACAAAGCCATCAATAAC
* *
2359303 GGTAATATGATTGGCACAAAGCCATCA
1 GGTAATATGATCGACACAAAGCCATCA
2359330 GTAGTATCAC
Statistics
Matches: 98, Mismatches: 25, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 98 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (32 bp):
GGTAATATGATCGACACAAAGCCATCAATAAC
Found at i:2359280 original size:64 final size:64
Alignment explanation
Indices: 2359175--2359332 Score: 181
Period size: 64 Copynumber: 2.5 Consensus size: 64
2359165 TAAACAGAAT
* ** ** * * *
2359175 GGTAATATGATTGGCACAAAGCCATCAGTAGCAGTGTTATGATCGGTACACAGTAATCAGTAAC
1 GGTAATATGATTGGCACAAAGCCATCAGTAACAGTAATATGATCGACACAAAGCAATCAATAAC
* * * * ** *
2359239 TGTAATATGATCGACACAAAGCCATCGGTAATGGTAATATGATCGACACAAAGCCATCAATAAC
1 GGTAATATGATTGGCACAAAGCCATCAGTAACAGTAATATGATCGACACAAAGCAATCAATAAC
2359303 GGTAATATGATTGGCACAAAGCCATCAGTA
1 GGTAATATGATTGGCACAAAGCCATCAGTA
2359333 GTATCACAGT
Statistics
Matches: 75, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
64 75 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.23
Consensus pattern (64 bp):
GGTAATATGATTGGCACAAAGCCATCAGTAACAGTAATATGATCGACACAAAGCAATCAATAAC
Found at i:2359379 original size:27 final size:25
Alignment explanation
Indices: 2359344--2359414 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 25
2359334 TATCACAGTA
*
2359344 AAGCTACCAGTAATAGTATATGTGGCC
1 AAGCCACCAGTAATAGTAT-TGTGG-C
2359371 AAGCCACCAGTAATAGTGATTGTGGC
1 AAGCCACCAGTAATAGT-ATTGTGGC
*
2359397 AGAGCCACCAAT-ATAGTA
1 A-AGCCACCAGTAATAGTA
2359415 CTTCCTCCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
25 1 0.03
26 7 0.17
27 30 0.75
28 2 0.05
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (25 bp):
AAGCCACCAGTAATAGTATTGTGGC
Found at i:2359549 original size:24 final size:24
Alignment explanation
Indices: 2359494--2359560 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
2359484 TCATACCAAA
*
2359494 CACAGACAAAGCAATCATTTACAT
1 CACAGACAAATCAATCATTTACAT
**
2359518 CA-AGGACAAATCAATCATTTATGT
1 CACA-GACAAATCAATCATTTACAT
* *
2359542 CACAGACAATTCAAACATT
1 CACAGACAAATCAATCATT
2359561 AACCTCGAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.03
24 34 0.94
25 1 0.03
ACGTcount: A:0.45, C:0.22, G:0.09, T:0.24
Consensus pattern (24 bp):
CACAGACAAATCAATCATTTACAT
Found at i:2359773 original size:27 final size:27
Alignment explanation
Indices: 2359707--2359912 Score: 141
Period size: 27 Copynumber: 7.7 Consensus size: 27
2359697 CCTAACAGAA
* * *
2359707 GTATTACAGTCATTTTACCCTATA-GA
1 GTATTACGGTCATTTTACCCTACAGGG
* * *
2359733 GCATTATGGTCATTTTATCCTACAGGG
1 GTATTACGGTCATTTTACCCTACAGGG
* *
2359760 GTATTACGGTCATTTTACCCTATAAGG
1 GTATTACGGTCATTTTACCCTACAGGG
* * **
2359787 GTATTATGGTTATTTTACCCTATGGGG
1 GTATTACGGTCATTTTACCCTACAGGG
* * * **
2359814 GTA-TATCGATCAATTCA-CCTAACTA-AA
1 GTATTA-CGGTCATTTTACCCT-AC-AGGG
* * *
2359841 GTATTACGGACATTTCACTCTACAGGG
1 GTATTACGGTCATTTTACCCTACAGGG
*
2359868 GCATTACGGTCATTTTACCCTACAGGG
1 GTATTACGGTCATTTTACCCTACAGGG
* * *
2359895 ATATTATGGGCATTTTAC
1 GTATTACGGTCATTTTAC
2359913 AAACATTAGG
Statistics
Matches: 135, Mismatches: 38, Indels: 13
0.73 0.20 0.07
Matches are distributed among these distances:
26 25 0.19
27 106 0.79
28 4 0.03
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (27 bp):
GTATTACGGTCATTTTACCCTACAGGG
Found at i:2372665 original size:42 final size:44
Alignment explanation
Indices: 2372618--2372716 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 44
2372608 ATGTTGGAAG
* *
2372618 TAAAATTAAAAAA-TAGTTACGTG-TT-TTTTATAAGTAACTATA
1 TAAAATTAAAAAATTA-TGACGTGTTTCTTTTATAAATAACTATA
* *
2372660 TAAAATTAAAAAATTATGATGTGTTTCTTTTATAAATAATTATA
1 TAAAATTAAAAAATTATGACGTGTTTCTTTTATAAATAACTATA
*
2372704 TGAAATTAAAAAA
1 TAAAATTAAAAAA
2372717 AAAATCCACA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 18 0.37
43 4 0.08
44 27 0.55
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.40
Consensus pattern (44 bp):
TAAAATTAAAAAATTATGACGTGTTTCTTTTATAAATAACTATA
Found at i:2374240 original size:23 final size:22
Alignment explanation
Indices: 2374197--2374240 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
2374187 TTATAGTCTA
*
2374197 ATTTTTATTTTGTTTATAAATT
1 ATTTTTATTTTGTTTAAAAATT
2374219 ATTTGTTATTTTAG-TTAAAAAT
1 ATTT-TTATTTT-GTTTAAAAAT
2374241 AAATTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 14 0.74
24 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
ATTTTTATTTTGTTTAAAAATT
Found at i:2378120 original size:36 final size:35
Alignment explanation
Indices: 2378080--2378182 Score: 104
Period size: 36 Copynumber: 2.9 Consensus size: 35
2378070 AAATAAATAA
*
2378080 ATATACATAATATATACGCAATATAGTA-CTAAGAAT
1 ATATACATAATATATA--CAATATAGTATCTAAAAAT
* * *
2378116 ATATATATACACATATACAATATAGTATTTAAAAAT
1 ATATACATA-ATATATACAATATAGTATCTAAAAAT
* *
2378152 ATATACATAATATTTAC-ATATA-TATATAAAA
1 ATATACATAATATATACAATATAGTATCTAAAA
2378183 TAAATATTGA
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
33 8 0.14
34 5 0.09
35 16 0.28
36 22 0.39
37 6 0.11
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.35
Consensus pattern (35 bp):
ATATACATAATATATACAATATAGTATCTAAAAAT
Found at i:2378184 original size:21 final size:21
Alignment explanation
Indices: 2378141--2378184 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2378131 TACAATATAG
*
2378141 TATTTAAAAATATATACATAA
1 TATTTAAAAATATATACAAAA
* * *
2378162 TATTTACATATATATATAAAA
1 TATTTAAAAATATATACAAAA
2378183 TA
1 TA
2378185 AATATTGAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
TATTTAAAAATATATACAAAA
Found at i:2379965 original size:42 final size:42
Alignment explanation
Indices: 2379862--2380056 Score: 197
Period size: 42 Copynumber: 4.7 Consensus size: 42
2379852 TTTTTTTTTC
* * *
2379862 GTCTGCTCCATTGA-TGCTTAGGGAGATAAGA-C--TGGATGT
1 GTCTGCTCCACT-ATTGCTTAGGGAGATAAGATCTGTGGTTCT
* * *
2379901 GATCTGCTCCACTACTGTTTAGGGAGATAAGATCTGTGGTTTT
1 G-TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTCT
* * * * * *
2379944 GTCCGCTCCGCTACTACTTAGGGAGATAAGA-CT-TGATGC-
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTCT
*
2379983 GATCTGCTCCATTATTGCTTAGGGAGATAAGATCTGTGGTTCT
1 G-TCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTCT
2380026 GTCTGCTCCACTATTGCTTAGGGAGATAAGA
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGA
2380057 CTTGCAACTT
Statistics
Matches: 128, Mismatches: 19, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
39 3 0.02
40 54 0.42
41 5 0.04
42 59 0.46
43 7 0.05
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (42 bp):
GTCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTCT
Found at i:2380059 original size:82 final size:81
Alignment explanation
Indices: 2379862--2380060 Score: 281
Period size: 82 Copynumber: 2.4 Consensus size: 81
2379852 TTTTTTTTTC
* * * *
2379862 GTCTGCTCCATTGATGCTTAGGGAGATAAGACTGGATGTGATCTGCTCCACTACTGTTTAGGGAG
1 GTCTGCTCCACT-ATGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAG
*
2379927 ATAAGATCTGTGGTTTT
65 ATAAGATCTGTGGTTCT
* * * * *
2379944 GTCCGCTCCGCTACTACTTAGGGAGATAAGACTTGATGCGATCTGCTCCATTATTGCTTAGGGAG
1 GTCTGCTCCACTA-TGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAG
2380009 ATAAGATCTGTGGTTCT
65 ATAAGATCTGTGGTTCT
2380026 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTG
1 GTCTGCTCCACTA-TGCTTAGGGAGATAAGACTTG
2380061 CAACTTTTGA
Statistics
Matches: 102, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
81 1 0.01
82 101 0.99
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.33
Consensus pattern (81 bp):
GTCTGCTCCACTATGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGA
TAAGATCTGTGGTTCT
Found at i:2380385 original size:72 final size:73
Alignment explanation
Indices: 2380240--2380420 Score: 285
Period size: 72 Copynumber: 2.5 Consensus size: 73
2380230 ACATGTGAAC
* *
2380240 TGAGGCTCAACTCACTTT-TCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCT
1 TGAGGCTCAACTCA-TTTCTCGCAATATGAGTTGA-TATTTTGAAAACAGAAATTGAAATTACCT
* *
2380304 CAGCGTGTCT
64 CAACATGTCT
2380314 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCA
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTTGAAAACAGAAATTGAAATTACCTCA
*
2380378 ATATGTCT
66 ACATGTCT
2380386 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAT
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAT
2380421 TCTTTCAAAA
Statistics
Matches: 100, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
72 67 0.67
73 3 0.03
74 30 0.30
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (73 bp):
TGAGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTTGAAAACAGAAATTGAAATTACCTCA
ACATGTCT
Found at i:2380618 original size:54 final size:55
Alignment explanation
Indices: 2380554--2380659 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 55
2380544 GCCCCGAGGC
* * *
2380554 TCAACTCACCTCTTGCAATATGAGCTGATT-TTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTCTTGAAAAA-CAGAAATTGAAAAGGT
* *
2380608 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATTCTTGAAAAACAGAAATTGAAAA
2380660 TACCTCAACG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
54 34 0.76
55 11 0.24
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (55 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTCTTGAAAAACAGAAATTGAAAAGGT
Found at i:2380725 original size:126 final size:126
Alignment explanation
Indices: 2380482--2380726 Score: 280
Period size: 127 Copynumber: 1.9 Consensus size: 126
2380472 GTCCTGAGGC
* * *
2380482 TCAACTCACCTCTCGCAGTATGAGTTGAAATTAAAACACAAAAAATGAAAATACCTCAGCGTGCC
1 TCAACCCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAAATGAAAATACCTCAACGTGCC
** * *
2380547 CCGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGT
66 CCGAGGCTCAACTCACCTCTCACAATATAAGCTGATTTTGAAAAAGCAGAAATTAAAAGGT
** * * *
2380608 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAA-ACAGAAATTGAAAATACCTCAACGTG
1 TCAACCCACCTCTCGCAATATGAGTTGA-AATT-AAAACACAAAAAATGAAAATACCTCAACGTG
* ** ** *
2380672 TCTTGAGGCTCAACTCATTTCTCACAATATAAGTTGAATTTTG-AAAA-CAGAAATT
64 CCCCGAGGCTCAACTCACCTCTCACAATATAAGCTG-ATTTTGAAAAAGCAGAAATT
2380727 GAAATTACCT
Statistics
Matches: 98, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
126 33 0.34
127 56 0.57
128 9 0.09
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (126 bp):
TCAACCCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAAATGAAAATACCTCAACGTGCC
CCGAGGCTCAACTCACCTCTCACAATATAAGCTGATTTTGAAAAAGCAGAAATTAAAAGGT
Found at i:2380736 original size:72 final size:74
Alignment explanation
Indices: 2380608--2380781 Score: 255
Period size: 72 Copynumber: 2.4 Consensus size: 74
2380598 ATTAAAAGGT
*
2380608 TCAACCCACCTCTCGCAATATGAGTTG-ATTCTTGACAAACAGAAATTGAAAATACCTCAACGTG
1 TCAACTCACCTCTCGCAATATGAGTTGAATTCTTGACAAACAGAAATTGAAAATACCTCAACGTG
*
2380672 TCTTGAGGC
66 TCCTGAGGC
** * * * *
2380681 TCAACTCATTTCTCACAATATAAGTTGAATT-TTGA-AAACAGAAATTGAAATTACCTCAGCGTG
1 TCAACTCACCTCTCGCAATATGAGTTGAATTCTTGACAAACAGAAATTGAAAATACCTCAACGTG
2380744 TCCTGAGGC
66 TCCTGAGGC
2380753 TCAACTCACCTCTCGCAATATGAGTTGAA
1 TCAACTCACCTCTCGCAATATGAGTTGAA
2380782 AAAAATACCA
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
72 59 0.67
73 26 0.30
74 3 0.03
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (74 bp):
TCAACTCACCTCTCGCAATATGAGTTGAATTCTTGACAAACAGAAATTGAAAATACCTCAACGTG
TCCTGAGGC
Found at i:2380960 original size:207 final size:202
Alignment explanation
Indices: 2380608--2380988 Score: 530
Period size: 207 Copynumber: 1.9 Consensus size: 202
2380598 ATTAAAAGGT
* *
2380608 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAAATACCTCAACGTGT
1 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAAAAACAGAAATTGAAAATACCTCAACGTGA
* ** *
2380673 CTTGAGGCTCAACTCATTTCTCACAATATAAGTTGAATTTTGAAAACAGAAATTGAAATTACCTC
66 CTCGAGGCTCAACTCACCTCTCACAATATAAGTTGAATTTTGAAAACAGAAATTGAAAATACCTC
* *
2380738 AGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAAAAAATACCACAGTGTGTAAT
131 AACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGAAAAAAATACCACAGTGTGTAAT
2380803 CTGAAGC
196 CTGAAGC
* * * * *
2380810 TCAACTCACCTTTCGCAATATGAGTTGATCTTTTTAAAAACAGAAATTGAAAATACCTCAGCATG
1 TCAACCCACCTCTCGCAATATGAGTTGAT-TCTTGAAAAACAGAAATTGAAAATACCTCA--ACG
* * *
2380875 TGAAC-CGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACATAAATTGAAAA
63 TG-ACTCGAGGCTCAACTCACCTCTCACAATATAAGTTGA--ATTTTGAAAACAGAAATTGAAAA
* **
2380939 TACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAA
125 TACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGAA
2380989 TTTTGAAAAC
Statistics
Matches: 154, Mismatches: 19, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
202 27 0.18
203 27 0.18
205 34 0.22
206 1 0.01
207 65 0.42
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.29
Consensus pattern (202 bp):
TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAAAAACAGAAATTGAAAATACCTCAACGTGA
CTCGAGGCTCAACTCACCTCTCACAATATAAGTTGAATTTTGAAAACAGAAATTGAAAATACCTC
AACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGAAAAAAATACCACAGTGTGTAAT
CTGAAGC
Found at i:2381023 original size:72 final size:72
Alignment explanation
Indices: 2380802--2381065 Score: 307
Period size: 72 Copynumber: 3.6 Consensus size: 72
2380792 CAGTGTGTAA
* * *
2380802 TCTGAAGCTCAACTCACCTT-TCGCAATATGAGTTGATCTTTTTAAAAACAGAAATTGAAAATAC
1 TCTGAGGCTCAACTCA-CTTCTCGCAATATAAGTTGAT-TTTTTGAAAACAGAAATTGAAAATAC
2380866 CTCAGCATGTG
64 CTCAGC--GTG
* * * *
2380877 AACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACATAAATTGAAAATAC
1 -TCTGAGGCTCAACTCACTTCTCGCAATATAAGTTGA-TTTTTTGAAAACAGAAATTGAAAATAC
*
2380942 CTCAACGTG
64 CTCAGCGTG
* * *
2380951 TCTTGAGGCTCAACTCATTTCTCGCAATATAAGTTGA-ATTTTGAAAACAGAAATTGAAATTACC
1 TC-TGAGGCTCAACTCACTTCTCGCAATATAAGTTGATTTTTTGAAAACAGAAATTGAAAATACC
2381015 TCAGCGTG
65 TCAGCGTG
* * * *
2381023 TCCTAAGGCTCAAATCATTTCTCGCAATATGAGTTGATTTTTT
1 T-CTGAGGCTCAACTCACTTCTCGCAATATAAGTTGATTTTTT
2381066 TTTGAAACAG
Statistics
Matches: 163, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
72 63 0.39
73 6 0.04
74 34 0.21
75 2 0.01
76 57 0.35
77 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (72 bp):
TCTGAGGCTCAACTCACTTCTCGCAATATAAGTTGATTTTTTGAAAACAGAAATTGAAAATACCT
CAGCGTG
Found at i:2384995 original size:36 final size:36
Alignment explanation
Indices: 2384948--2385100 Score: 171
Period size: 36 Copynumber: 4.0 Consensus size: 36
2384938 CTAAGCTACC
2384948 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGT
1 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGT
*
2384984 ACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCT
1 ACTTATCACTTTGTCACTTGATCAGATAA--GT-G-T--AG-T
* * *
2385027 ACCACTTATCACTTTGTCTCTTGATCAGATAAATGTAGC
1 ---ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGT
*
2385066 ACTTATCACTTTGTTACTTGATCAGATAAGTGTAG
1 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
2385101 ATAAAGCTAC
Statistics
Matches: 99, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
36 60 0.61
38 2 0.02
39 1 0.01
40 3 0.03
42 3 0.03
43 2 0.02
44 1 0.01
46 27 0.27
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (36 bp):
ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGT
Found at i:2385035 original size:46 final size:45
Alignment explanation
Indices: 2384984--2385133 Score: 149
Period size: 46 Copynumber: 3.5 Consensus size: 45
2384974 TAAGTGTAGT
2384984 ACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACC
1 ACTTATCACTTTTTCACTTGATCAGATAAGTGTAG-TAAAGCTACC
* * *
2385030 ACTTATCACTTTGTCTCTTGATCAGATAA----A-T---G-TAGC
1 ACTTATCACTTTTTCACTTGATCAGATAAGTGTAGTAAAGCTACC
2385066 ACTTATCACTTTGTT-ACTTGATCAGATAAGTGTAGATAAAGCTACC
1 ACTTATCACTTT-TTCACTTGATCAGATAAGTGTAG-TAAAGCTACC
* * *
2385112 ACTTATCTCTTTATCTCTTGAT
1 ACTTATCACTTTTTCACTTGAT
2385134 TAGAAGTACT
Statistics
Matches: 83, Mismatches: 9, Indels: 24
0.72 0.08 0.21
Matches are distributed among these distances:
36 28 0.34
37 2 0.02
40 2 0.02
42 2 0.02
45 2 0.02
46 47 0.57
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.39
Consensus pattern (45 bp):
ACTTATCACTTTTTCACTTGATCAGATAAGTGTAGTAAAGCTACC
Found at i:2385043 original size:82 final size:82
Alignment explanation
Indices: 2384921--2385133 Score: 349
Period size: 82 Copynumber: 2.6 Consensus size: 82
2384911 CATTTGTCCA
* * *
2384921 TGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGTA
1 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGATCAGATAAATGTAGCA
2384985 CTTATCACTTT-TTCACT
66 CTTATCACTTTGTT-ACT
2385002 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGATCAGATAAATGTAGCA
1 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGATCAGATAAATGTAGCA
2385067 CTTATCACTTTGTTACT
66 CTTATCACTTTGTTACT
* * *
2385084 TGATCAGATAAGTGTAGATAAAGCTACCACTTATCTCTTTATCTCTTGAT
1 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGAT
2385134 TAGAAGTACT
Statistics
Matches: 124, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
81 19 0.15
82 103 0.83
83 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (82 bp):
TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGATCAGATAAATGTAGCA
CTTATCACTTTGTTACT
Found at i:2390095 original size:23 final size:23
Alignment explanation
Indices: 2390069--2390119 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
2390059 TGTTATTGAT
2390069 CAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATAA
*
2390092 CAGTGGTAGCTTCGGCTACATAT
1 CAGTGGTAGCTTCGGCTACATAA
2390115 CAGTG
1 CAGTG
2390120 TTGCACTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (23 bp):
CAGTGGTAGCTTCGGCTACATAA
Found at i:2396707 original size:28 final size:27
Alignment explanation
Indices: 2396642--2396707 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
2396632 TTTGACAGTA
* *
2396642 ACAGTACAGTGTAGGCCTTAGCCCTAT
1 ACAGTACAGTGTAGGCCTAAGCCCGAT
**
2396669 ACAAAAACAGTGTAGGCCTAAGCCCGAT
1 AC-AGTACAGTGTAGGCCTAAGCCCGAT
2396697 ACAGTATCAGT
1 ACAGTA-CAGT
2396708 ATGCTGCAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 4 0.13
28 27 0.87
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.21
Consensus pattern (27 bp):
ACAGTACAGTGTAGGCCTAAGCCCGAT
Found at i:2396916 original size:22 final size:22
Alignment explanation
Indices: 2396862--2396926 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
2396852 TACCATTAAT
2396862 CAGAATGGCTAAAAG-TCATAAA
1 CAGAATGGCTAAAAGCT-ATAAA
* *
2396884 CA-AGATAGCTATAAGCTATAAA
1 CAGA-ATGGCTAAAAGCTATAAA
* *
2396906 CAGAATGGCTACAAGCCATAA
1 CAGAATGGCTAAAAGCTATAA
2396927 GTACATTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 1 0.03
22 32 0.91
23 2 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (22 bp):
CAGAATGGCTAAAAGCTATAAA
Found at i:2396988 original size:32 final size:32
Alignment explanation
Indices: 2396918--2397056 Score: 145
Period size: 32 Copynumber: 4.4 Consensus size: 32
2396908 GAATGGCTAC
* *
2396918 AAGCCATAAGT-ACATTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATTGGCACA
* * * *
2396949 AAACCATCAGTAGCAGTGATATAATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATTGGCACA
* * ** * *
2396981 CAGCCATCAATAATGGTAATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATTGGCACA
*
2397013 AAGCCATCAGTAACGGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATTGGCACA
*
2397045 AAGCCAACAGTA
1 AAGCCATCAGTA
2397057 GCATTGCAGG
Statistics
Matches: 85, Mismatches: 22, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
31 9 0.11
32 76 0.89
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATTGGCACA
Found at i:2397299 original size:24 final size:24
Alignment explanation
Indices: 2397244--2397300 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
2397234 TCATACCAAA
*
2397244 CACAGACAAAGCAATCATTTACAT
1 CACAGACAAAGAAATCATTTACAT
* *
2397268 CA-AGGACAAATAAATCATTTATAT
1 CACA-GACAAAGAAATCATTTACAT
2397292 CACAGACAA
1 CACAGACAA
2397301 TTCAAACATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 1 0.04
24 26 0.93
25 1 0.04
ACGTcount: A:0.49, C:0.21, G:0.09, T:0.21
Consensus pattern (24 bp):
CACAGACAAAGAAATCATTTACAT
Found at i:2397433 original size:27 final size:27
Alignment explanation
Indices: 2397378--2397583 Score: 164
Period size: 27 Copynumber: 7.6 Consensus size: 27
2397368 TAGCAAAGGC
* ** *
2397378 ATTACGGTCACTTTATGCTACAGGAGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
2397405 ATTACGATCATTTTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
** * * **
2397432 A-TATCAATCAATTCA-CCTACCAGAAGT
1 ATTA-CGGTCATTTTACCCTA-CAGGGGT
*
2397459 ATTACAGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* **
2397486 ATTATGGTCATTTTACCCTATTGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * **
2397513 ATTACGGTTATTTCACCCTACAATGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* **
2397540 ATTACGGTTATTTTACCCTACATGGGAC
1 ATTACGGTCATTTTACCCTACA-GGGGT
2397568 ATTACGGTCATTTTAC
1 ATTACGGTCATTTTAC
2397584 AAACATTGGG
Statistics
Matches: 140, Mismatches: 34, Indels: 9
0.77 0.19 0.05
Matches are distributed among these distances:
26 6 0.04
27 112 0.80
28 22 0.16
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAGGGGT
Found at i:2397528 original size:81 final size:79
Alignment explanation
Indices: 2397330--2397583 Score: 251
Period size: 81 Copynumber: 3.1 Consensus size: 79
2397320 GGCCAAAATA
* * * *
2397330 GTCATTTTACCCT-TTGAGGGTATATTGGTCAATTCACCTAGCAAAGGCATTACGGTCACTTTAT
1 GTCATTTTACCCTATTG-GGGTATATCGGTCAATTCACCTA-CAAA-GTATTACGGTCATTTTAC
* *
2397394 GCTACAGGAGTATTACG
63 CCTACAGGGGTATTACG
* * ** *
2397411 ATCATTTTACCCTATAGGGGTATATCAATCAATTCACCTACCAGAAGTATTACAGTCATTTTACC
1 GTCATTTTACCCTATTGGGGTATATCGGTCAATTCACCTA-CA-AAGTATTACGGTCATTTTACC
*
2397476 CTACAGGGGTATTATG
64 CTACAGGGGTATTACG
* * * *
2397492 GTCATTTTACCCTATTGGGGTAT-TACGGTTATTTCACCCTACAATGGTATTACGGTTATTTTAC
1 GTCATTTTACCCTATTGGGGTATAT-CGGTCAATTCA-CCTACAA-AGTATTACGGTCATTTTAC
**
2397556 CCTACATGGGACATTACG
63 CCTACA-GGGGTATTACG
2397574 GTCATTTTAC
1 GTCATTTTAC
2397584 AAACATTGGG
Statistics
Matches: 142, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
80 2 0.01
81 114 0.80
82 26 0.18
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.35
Consensus pattern (79 bp):
GTCATTTTACCCTATTGGGGTATATCGGTCAATTCACCTACAAAGTATTACGGTCATTTTACCCT
ACAGGGGTATTACG
Found at i:2399201 original size:45 final size:45
Alignment explanation
Indices: 2399137--2399226 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
2399127 ATAAAGTCCT
2399137 CCAAATCCTTATCCCATGAATCACTCCCCCAAGACCAATTCCACA
1 CCAAATCCTTATCCCATGAATCACTCCCCCAAGACCAATTCCACA
*
2399182 CCAAATCTTTATCCCATGAATCACTCCCCCAAGACCAATTCCACA
1 CCAAATCCTTATCCCATGAATCACTCCCCCAAGACCAATTCCACA
2399227 ACCACCTGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.33, C:0.41, G:0.04, T:0.21
Consensus pattern (45 bp):
CCAAATCCTTATCCCATGAATCACTCCCCCAAGACCAATTCCACA
Found at i:2407443 original size:5 final size:5
Alignment explanation
Indices: 2407433--2407515 Score: 123
Period size: 5 Copynumber: 16.8 Consensus size: 5
2407423 TGAAAAATAA
2407433 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
* * * *
2407483 ATATG ATATA ATATA ATATA ATATA ATAT- ATAT
1 ATATG ATATG ATATG ATATG ATATG ATATG ATAT
2407516 TCATTTAATA
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
4 4 0.05
5 73 0.95
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (5 bp):
ATATG
Found at i:2409686 original size:66 final size:65
Alignment explanation
Indices: 2409604--2409735 Score: 246
Period size: 66 Copynumber: 2.0 Consensus size: 65
2409594 CTTTTATGGA
*
2409604 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTATAGTCAATTTTAGACCATTAAATATAGTA
1 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCA-TAAATATAGTA
2409669 T
65 T
2409670 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATAAATATAGTAT
1 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATAAATATAGTAT
2409735 T
1 T
2409736 TCTATTTATG
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
65 13 0.20
66 52 0.80
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (65 bp):
TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATAAATATAGTAT
Found at i:2413073 original size:42 final size:42
Alignment explanation
Indices: 2413027--2413227 Score: 280
Period size: 42 Copynumber: 4.8 Consensus size: 42
2413017 TTTTGTGTAT
* * *
2413027 GTGAAATAATTTCAGACTTTACGTCGAGCAGGCTTATTGCCA
1 GTGAAACAATTTCAGACTTTACGTCTAGCAGGCTTAATGCCA
* *
2413069 GTGAAACAATATCAGACTTTACGTCTAGCAGACTTAATGCCA
1 GTGAAACAATTTCAGACTTTACGTCTAGCAGGCTTAATGCCA
* * *
2413111 GTGAAATAATTTCAGACTTTACGTTTAGCAGGCTTAATGCCG
1 GTGAAACAATTTCAGACTTTACGTCTAGCAGGCTTAATGCCA
*
2413153 GTGAAACAATATT-AGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGAAACAAT-TTCAGACTTTACGTCTAGCAGGCTTAATGCCA
* *
2413195 GTGAAAC-ATTTCAGACTATATGTCTAGCAGGCT
1 GTGAAACAATTTCAGACTTTACGTCTAGCAGGCT
2413228 AAGTGTCGGT
Statistics
Matches: 143, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
40 2 0.01
41 21 0.15
42 118 0.83
43 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (42 bp):
GTGAAACAATTTCAGACTTTACGTCTAGCAGGCTTAATGCCA
Found at i:2414472 original size:44 final size:44
Alignment explanation
Indices: 2414407--2414906 Score: 190
Period size: 44 Copynumber: 10.6 Consensus size: 44
2414397 AATTCGCTGT
* * *
2414407 CTTCAGTCTACTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGG
* * *
2414451 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG----G-C-----TGGTGG
* * * * ** * * ** * *
2414505 CTTTATTTTGTTCCACTGCAACGCCAGAGAAATAAGATTCGTTGT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGCT-GGTGG
* * **
2414550 CTTCAGTCTGCTCCGCTATAACTTCAGGGAGATAAGGCTGGTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGG
* * * *
2414594 CTTCAATCTGCTCTACTGCAACTTCAGGAAGATAAGATTTGCCATAATTTGTAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG----G-C-----TGGTGG
* * * ** * ** * *
2414648 CTTTAATCTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGCT-GGTGG
* *
2414693 CTTCAGTCTGCTCAACTGCAACTTCAGGGAGATAAGGCTGGTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGG
* * * *
2414737 CTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCCACCATAATTGGTAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG-----GC-----TGGTGG
** ** * * ** * *
2414791 CTTTGATCTGCTCCACTGCAACGCCAAGGAAATAAGATTCGCTGT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGCT-GGTGG
* * * * *
2414836 CTTCAGTCTGCTCCGCTGCAACTTTAAGGAGATAAGGCTAGTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGG
2414880 CTTCAATCTGCTCCACTGCAACTTCAG
1 CTTCAATCTGCTCCACTGCAACTTCAG
2414907 AATGATAAGA
Statistics
Matches: 317, Mismatches: 106, Indels: 66
0.65 0.22 0.13
Matches are distributed among these distances:
44 128 0.40
45 88 0.28
48 2 0.01
49 3 0.01
54 96 0.30
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGCTGGTGG
Found at i:2414564 original size:143 final size:143
Alignment explanation
Indices: 2414304--2414929 Score: 986
Period size: 143 Copynumber: 4.4 Consensus size: 143
2414294 TGTTACACTA
* *
2414304 GTGGCTTCAATCTGCTCCACTACAACTTTAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAAT
1 GTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAAT
* * * *
2414369 ATGTTCCACTGCAACGCCAGGGAAATAAAATTCGCTGTCTTCAGTCTACTCCGCTGCAACTTCAG
66 CTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAG
2414434 GGAGATAAGGCTG
131 GGAGATAAGGCTG
*
2414447 GTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTATT
1 GTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAAT
* * **
2414512 TTGTTCCACTGCAACGCCAGAGAAATAAGATTCGTTGTCTTCAGTCTGCTCCGCTATAACTTCAG
66 CTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAG
2414577 GGAGATAAGGCTG
131 GGAGATAAGGCTG
* **
2414590 GTGGCTTCAATCTGCTCTACTGCAACTTCAGGAAGATAAGATTTGCCATAATTTGTAGCTTTAAT
1 GTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAAT
* * **
2414655 CTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCAACTGCAACTTCAG
66 CTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAG
2414720 GGAGATAAGGCTG
131 GGAGATAAGGCTG
* * * *
2414733 GTGGCTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCCACCATAATTGGTAGCTTTGAT
1 GTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAAT
* *
2414798 CTGCTCCACTGCAACGCCA-AGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTTA
66 CTGTTCCACTGCAACGCCAGA-GAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCA
* *
2414862 AGGAGATAAGGCTA
130 GGGAGATAAGGCTG
2414876 GTGGCTTCAATCTGCTCCACTGCAACTTCA-GAATGATAAGATCCGCCATAATTT
1 GTGGCTTCAATCTGCTCCACTGCAACTTCAGGAA-GATAAGATCCGCCATAATTT
2414930 CTTCAATCAA
Statistics
Matches: 441, Mismatches: 40, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
142 3 0.01
143 438 0.99
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (143 bp):
GTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAAT
CTGTTCCACTGCAACGCCAGAGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAG
GGAGATAAGGCTG
Found at i:2414865 original size:45 final size:44
Alignment explanation
Indices: 2414796--2414905 Score: 121
Period size: 45 Copynumber: 2.5 Consensus size: 44
2414786 GGTAGCTTTG
** * * *
2414796 ATCTGCTCCACTGCAACGCCAAGGAAATAAGATTCGCTGTCTTCA
1 ATCTGCTCCACTGCAACTTCAAGGAAATAAGACTAG-TGGCTTCA
* * * * *
2414841 GTCTGCTCCGCTGCAACTTTAAGGAGATAAGGCTAGTGGCTTCA
1 ATCTGCTCCACTGCAACTTCAAGGAAATAAGACTAGTGGCTTCA
2414885 ATCTGCTCCACTGCAACTTCA
1 ATCTGCTCCACTGCAACTTCA
2414906 GAATGATAAG
Statistics
Matches: 52, Mismatches: 13, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
44 25 0.48
45 27 0.52
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAAGGAAATAAGACTAGTGGCTTCA
Found at i:2418556 original size:6 final size:6
Alignment explanation
Indices: 2418545--2418606 Score: 81
Period size: 6 Copynumber: 10.0 Consensus size: 6
2418535 TTGGTCTCTC
2418545 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C-TTTT CTTTTTCT CCTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C-TTTT-T -CTTTTT
*
2418595 ATTTTT CTTTTT
1 CTTTTT CTTTTT
2418607 TGTTTTTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
5 5 0.10
6 35 0.70
7 4 0.08
8 5 0.10
9 1 0.02
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:2428854 original size:60 final size:61
Alignment explanation
Indices: 2428769--2428910 Score: 146
Period size: 60 Copynumber: 2.3 Consensus size: 61
2428759 CCTTTCCTTT
* * * * **
2428769 TTGAAATTTTTAGAATTAGAGCT-AAATTATCATATTATGTAAATGTTGAGAGCTAAATTTA
1 TTGAATTTTTTAGAATTAGAACTAAAATGA-CAAATTATGTAAACATTGAGAGCTAAATTTA
* * * *
2428830 TTG-ATTTTTTAGAATTCA-AACTAAAATGACAAATTTTGTAAACATTGAGGGTTAAATTTG
1 TTGAATTTTTTAGAATT-AGAACTAAAATGACAAATTATGTAAACATTGAGAGCTAAATTTA
*
2428890 TTGAATTTTTTAGATTTAGAA
1 TTGAATTTTTTAGAATTAGAA
2428911 TCAAAACGAT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
60 43 0.65
61 23 0.35
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (61 bp):
TTGAATTTTTTAGAATTAGAACTAAAATGACAAATTATGTAAACATTGAGAGCTAAATTTA
Found at i:2437812 original size:30 final size:30
Alignment explanation
Indices: 2437756--2437812 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
2437746 TTATTCTTTG
* **
2437756 ACGGATTAAATTATAAATTTTTATTTTTAA
1 ACGGATCAAATTATAAATTTAAATTTTTAA
*
2437786 ACGGATCAAATTTTAAATTTAAATTTT
1 ACGGATCAAATTATAAATTTAAATTTT
2437813 AAAGAGGTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (30 bp):
ACGGATCAAATTATAAATTTAAATTTTTAA
Found at i:2440753 original size:31 final size:30
Alignment explanation
Indices: 2440718--2440804 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
2440708 CAAATTAAAG
* *
2440718 AAATTTATAAATATAAAGGATTAAATTTATT
1 AAATTTATAAATATTAAGGATTAAATTGA-T
*
2440749 AAATTATTTAAA-ATTAA-GATTAAATTGAT
1 AAATT-TATAAATATTAAGGATTAAATTGAT
* *
2440778 AGAATATATAAATATTGAGGATTAAAT
1 A-AATTTATAAATATTAAGGATTAAAT
2440805 ATGAATTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
29 7 0.15
30 17 0.37
31 17 0.37
32 5 0.11
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (30 bp):
AAATTTATAAATATTAAGGATTAAATTGAT
Found at i:2444449 original size:20 final size:20
Alignment explanation
Indices: 2444424--2444463 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2444414 GAATGAACTT
*
2444424 ATTATTTTGCTTTTTAACCA
1 ATTATTTTGCTTTTGAACCA
*
2444444 ATTATTTTGGTTTTGAACCA
1 ATTATTTTGCTTTTGAACCA
2444464 TCCCTATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (20 bp):
ATTATTTTGCTTTTGAACCA
Found at i:2445275 original size:43 final size:43
Alignment explanation
Indices: 2445214--2445300 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
2445204 TCCCTCAAGG
2445214 TGTTCCACCAGAGTGTAAACGCCCAAGGTTCTAAAATCAAACC
1 TGTTCCACCAGAGTGTAAACGCCCAAGGTTCTAAAATCAAACC
*
2445257 TGTTCCACCAGAGTGTAAACGCCCAGGGTTCTAAAATCAAACC
1 TGTTCCACCAGAGTGTAAACGCCCAAGGTTCTAAAATCAAACC
2445300 T
1 T
2445301 CTCCTCTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (43 bp):
TGTTCCACCAGAGTGTAAACGCCCAAGGTTCTAAAATCAAACC
Found at i:2447117 original size:26 final size:27
Alignment explanation
Indices: 2447068--2447118 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
2447058 AATAACTAAA
* *
2447068 TAAATAATTAAAAATTCATAAAATTTT
1 TAAAGAATAAAAAATTCATAAAATTTT
*
2447095 TAAAGAATAAAAAATT-ATTAAATT
1 TAAAGAATAAAAAATTCATAAAATT
2447119 GGTTCAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (27 bp):
TAAAGAATAAAAAATTCATAAAATTTT
Found at i:2452904 original size:70 final size:67
Alignment explanation
Indices: 2452806--2452937 Score: 167
Period size: 70 Copynumber: 1.9 Consensus size: 67
2452796 CCGAATAAAT
* * * *
2452806 AAAGGCAAAACTACGTCATTTTGATAAATGTTTACCTATTCTAAAGTTAAAAGTCAAAATCATTA
1 AAAGGCAAAACTACATCATTTTGATAAATATTTA-CTAAT-T-AAGTTAAAAGGCAAAATCATTA
2452871 AGTTA
63 AGTTA
* *
2452876 AAAGGCAAAACTATAT-AGTTTTGATAAATATTTACTAATTAAGTTAAAAGGCAAAATTATTA
1 AAAGGCAAAACTACATCA-TTTTGATAAATATTTACTAATTAAGTTAAAAGGCAAAATCATTA
2452938 TATTTGTTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
67 20 0.36
68 1 0.02
69 5 0.09
70 29 0.53
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.33
Consensus pattern (67 bp):
AAAGGCAAAACTACATCATTTTGATAAATATTTACTAATTAAGTTAAAAGGCAAAATCATTAAGT
TA
Found at i:2456189 original size:5 final size:6
Alignment explanation
Indices: 2456171--2456196 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2456161 AAAAAATATA
2456171 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
2456197 TTGAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:2460215 original size:24 final size:23
Alignment explanation
Indices: 2460172--2460217 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2460162 AGTGTTGTTA
*
2460172 ATATATTTTGAAAACAAATTTAG
1 ATATATTCTGAAAACAAATTTAG
2460195 ATATATTACTGAAAATC-AATTTA
1 ATATATT-CTGAAAA-CAAATTTA
2460218 TTTTCCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 12 0.60
25 1 0.05
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (23 bp):
ATATATTCTGAAAACAAATTTAG
Found at i:2461894 original size:6 final size:6
Alignment explanation
Indices: 2461885--2461909 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2461875 TTATAATTAT
2461885 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
2461910 CAATTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:2461964 original size:20 final size:21
Alignment explanation
Indices: 2461926--2461966 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2461916 TATTATATAA
*
2461926 ATATTTTTTATTTAACACATTC
1 ATATTTTATATTT-ACACATTC
2461948 ATATTTTATATTT-CACATT
1 ATATTTTATATTTACACATT
2461967 TCGACTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (21 bp):
ATATTTTATATTTACACATTC
Found at i:2467288 original size:24 final size:23
Alignment explanation
Indices: 2467245--2467290 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2467235 AGTGTTGTTA
*
2467245 ATATATTTTGAAAACAAATTTAG
1 ATATATTCTGAAAACAAATTTAG
2467268 ATATATTACTGAAAATC-AATTTA
1 ATATATT-CTGAAAA-CAAATTTA
2467291 TTTTCCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 12 0.60
25 1 0.05
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (23 bp):
ATATATTCTGAAAACAAATTTAG
Found at i:2470160 original size:46 final size:46
Alignment explanation
Indices: 2470060--2470263 Score: 342
Period size: 46 Copynumber: 4.5 Consensus size: 46
2470050 CTTACGTATG
* *
2470060 ACCACTTATCAC-TTGTC-CTTGAACAGATAAGTGTACCT-AGGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
*
2470103 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGTTAAGGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
*
2470149 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGTT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
*
2470195 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
2470241 ACCACTTATCACTTTGTCACTTG
1 ACCACTTATCACTTTGTCACTTG
2470264 TCACTGATCA
Statistics
Matches: 151, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
43 12 0.08
44 5 0.03
45 18 0.12
46 116 0.77
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.34
Consensus pattern (46 bp):
ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
Found at i:2472515 original size:17 final size:17
Alignment explanation
Indices: 2472473--2472515 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
2472463 ATAGTTTATA
2472473 TATATTTTATATACATT
1 TATATTTTATATACATT
* * *
2472490 CATATTTTTTATGATATT
1 TATATTTTATAT-ACATT
2472508 TATATTTT
1 TATATTTT
2472516 CATGTTTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (17 bp):
TATATTTTATATACATT
Found at i:2474093 original size:17 final size:17
Alignment explanation
Indices: 2474071--2474103 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2474061 TTTAAAATTT
2474071 TAATTTGGATTTTTAAA
1 TAATTTGGATTTTTAAA
*
2474088 TAATTTGTATTTTTAA
1 TAATTTGGATTTTTAA
2474104 CGCCTTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (17 bp):
TAATTTGGATTTTTAAA
Found at i:2475535 original size:24 final size:24
Alignment explanation
Indices: 2475507--2475558 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2475497 TTCGTAGGTA
** *
2475507 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTACACTAATAAATACT
* *
2475531 AAATATATTACACTAATAAGTACT
1 AAATAAATTACACTAATAAATACT
2475555 AAAT
1 AAAT
2475559 CTTCTAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.33
Consensus pattern (24 bp):
AAATAAATTACACTAATAAATACT
Found at i:2477686 original size:16 final size:16
Alignment explanation
Indices: 2477653--2477686 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2477643 AATTTTTGTT
* *
2477653 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
2477669 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
2477685 AA
1 AA
2477687 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:2480513 original size:21 final size:21
Alignment explanation
Indices: 2480487--2480527 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2480477 AGACGAGCAA
* *
2480487 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2480508 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2480528 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:2489905 original size:31 final size:31
Alignment explanation
Indices: 2489870--2490028 Score: 164
Period size: 31 Copynumber: 5.3 Consensus size: 31
2489860 TTCATTTGAA
* *
2489870 TTGATTTGTTTATGGTTATACATTGCCGAAT
1 TTGATTTGTATATGGATATACATTGCCGAAT
*
2489901 TTGATTTGTATATGGATATACATTGCTGAA-
1 TTGATTTGTATATGGATATACATTGCCGAAT
* * * * *
2489931 TTAATTTATATATGGTTATACATTACCAAAT
1 TTGATTTGTATATGGATATACATTGCCGAAT
* *
2489962 TTGATTTGTATAT--ATATACATTGACAAAT
1 TTGATTTGTATATGGATATACATTGCCGAAT
* * **
2489991 TTGATTCGTATATGGATATATATCACCGAA-
1 TTGATTTGTATATGGATATACATTGCCGAAT
2490021 TTGATTTG
1 TTGATTTG
2490029 AGCTTTGGAT
Statistics
Matches: 104, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
29 25 0.24
30 31 0.30
31 48 0.46
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (31 bp):
TTGATTTGTATATGGATATACATTGCCGAAT
Found at i:2489945 original size:61 final size:59
Alignment explanation
Indices: 2489866--2489984 Score: 175
Period size: 61 Copynumber: 2.0 Consensus size: 59
2489856 TGTCTTCATT
* * * * *
2489866 TGAATTGATTTGTTTATGGTTATACATTGCCGAATTTGATTTGTATATGGATATACATTGC
1 TGAATTAATTTATATATGGTTATACATTACCAAATTTGATTTGTATAT--ATATACATTGC
2489927 TGAATTAATTTATATATGGTTATACATTACCAAATTTGATTTGTATATATATACATTG
1 TGAATTAATTTATATATGGTTATACATTACCAAATTTGATTTGTATATATATACATTG
2489985 ACAAATTTGA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
59 10 0.19
61 43 0.81
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (59 bp):
TGAATTAATTTATATATGGTTATACATTACCAAATTTGATTTGTATATATATACATTGC
Found at i:2500645 original size:18 final size:18
Alignment explanation
Indices: 2500622--2500688 Score: 82
Period size: 18 Copynumber: 3.7 Consensus size: 18
2500612 GTAGTGATTC
2500622 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
2500640 AATTCGAG-TAATTCGGTT
1 AATTCG-GTTAATTCGGGT
* *
2500658 AATTCGGGTAATTTGGGT
1 AATTCGGTTAATTCGGGT
*
2500676 AATTCGATTAATT
1 AATTCGGTTAATT
2500689 TTTAACCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
17 1 0.02
18 40 0.95
19 1 0.02
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:2500654 original size:27 final size:27
Alignment explanation
Indices: 2500622--2500688 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
2500612 GTAGTGATTC
2500622 AATTCGGTTAATTCGGGTAATTCGAGT
1 AATTCGGTTAATTCGGGTAATTCGAGT
* *
2500649 AATTCGGTTAATTCGGGTAATTTGGGT
1 AATTCGGTTAATTCGGGTAATTCGAGT
*
2500676 AATTCGATTAATT
1 AATTCGGTTAATT
2500689 TTTAACCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (27 bp):
AATTCGGTTAATTCGGGTAATTCGAGT
Found at i:2500688 original size:9 final size:9
Alignment explanation
Indices: 2500622--2500681 Score: 84
Period size: 9 Copynumber: 6.7 Consensus size: 9
2500612 GTAGTGATTC
*
2500622 AATTCGGTT
1 AATTCGGGT
2500631 AATTCGGGT
1 AATTCGGGT
*
2500640 AATTCGAGT
1 AATTCGGGT
*
2500649 AATTCGGTT
1 AATTCGGGT
2500658 AATTCGGGT
1 AATTCGGGT
*
2500667 AATTTGGGT
1 AATTCGGGT
2500676 AATTCG
1 AATTCG
2500682 ATTAATTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 44 1.00
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.38
Consensus pattern (9 bp):
AATTCGGGT
Found at i:2507576 original size:11 final size:13
Alignment explanation
Indices: 2507552--2507583 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2507542 TAGTTCATTA
2507552 ATATTTTAATATG
1 ATATTTTAATATG
2507565 AT-TTTTAA-ATG
1 ATATTTTAATATG
2507576 ATATTTTA
1 ATATTTTA
2507584 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:2509820 original size:3 final size:3
Alignment explanation
Indices: 2509809--2509905 Score: 90
Period size: 3 Copynumber: 32.3 Consensus size: 3
2509799 ATTATTTTGT
*
2509809 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* * * * * *
2509854 TCT- TTA CTA TTA TTG TTA GTA TTA TTA CTA CTA TTA TTA TTA CTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2509899 TCA TTA T
1 TTA TTA T
2509906 ATTTACACCT
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
2 3 0.04
3 69 0.91
4 4 0.05
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2510081 original size:36 final size:34
Alignment explanation
Indices: 2510041--2510109 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
2510031 CATATTTTCG
* *
2510041 TATATTTTTTAATTTGTATATACATATACTTATATC
1 TATATTTTCTAATTT-T-TATAAATATACTTATATC
*
2510077 TATATTTTCTAATTTTTATAAATATATTTATAT
1 TATATTTTCTAATTTTTATAAATATACTTATAT
2510110 GTACATACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 15 0.50
35 1 0.03
36 14 0.47
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.58
Consensus pattern (34 bp):
TATATTTTCTAATTTTTATAAATATACTTATATC
Found at i:2510229 original size:13 final size:13
Alignment explanation
Indices: 2510206--2510240 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
2510196 AATATCACTA
2510206 TTTACTTTTTTATT
1 TTTA-TTTTTTATT
2510220 TTTATTTTTTATT
1 TTTATTTTTTATT
*
2510233 ATTATTTT
1 TTTATTTT
2510241 CAAATTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTTTTATT
Found at i:2521718 original size:3 final size:3
Alignment explanation
Indices: 2521707--2521806 Score: 96
Period size: 3 Copynumber: 33.3 Consensus size: 3
2521697 ATTATTTTGT
*
2521707 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
* * * * *
2521752 TTA TCT- TTA CTA TTA TTG TTA GTA TTA TTA CTA CTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
2521797 CTA TCA TTA T
1 TTA TTA TTA T
2521807 ATTTACACCT
Statistics
Matches: 79, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
2 3 0.04
3 72 0.91
4 4 0.05
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2521991 original size:36 final size:34
Alignment explanation
Indices: 2521942--2522010 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
2521932 CATATTTTCG
* *
2521942 TATATTTTTTAATTTGTATATACATATACTTATATC
1 TATATTTTCTAATTT-T-TATAAATATACTTATATC
*
2521978 TATATTTTCTAATTTTTATAAATATATTTATAT
1 TATATTTTCTAATTTTTATAAATATACTTATAT
2522011 GTACATACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 15 0.50
35 1 0.03
36 14 0.47
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.58
Consensus pattern (34 bp):
TATATTTTCTAATTTTTATAAATATACTTATATC
Found at i:2531749 original size:12 final size:12
Alignment explanation
Indices: 2531732--2531757 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2531722 TAATCATTGT
2531732 AATCATAATGAC
1 AATCATAATGAC
2531744 AATCATAATGAC
1 AATCATAATGAC
2531756 AA
1 AA
2531758 AAGAAAGAAA
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:0.15, G:0.08, T:0.23
Consensus pattern (12 bp):
AATCATAATGAC
Found at i:2532252 original size:22 final size:22
Alignment explanation
Indices: 2532224--2532267 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2532214 TAACTTCGGT
2532224 CACAAACAAAATTTTTTACTTA
1 CACAAACAAAATTTTTTACTTA
2532246 CACAAACAAAATTTTTTACTTA
1 CACAAACAAAATTTTTTACTTA
2532268 GTTATTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (22 bp):
CACAAACAAAATTTTTTACTTA
Found at i:2539069 original size:20 final size:20
Alignment explanation
Indices: 2539040--2539082 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2539030 AAAATAAACA
* **
2539040 TATAATTATTCATTTAATAT
1 TATAAGTATTCAAATAATAT
2539060 TATAAGTATTCAAATAATAT
1 TATAAGTATTCAAATAATAT
2539080 TAT
1 TAT
2539083 TTAAATAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (20 bp):
TATAAGTATTCAAATAATAT
Found at i:2542298 original size:221 final size:216
Alignment explanation
Indices: 2541920--2542337 Score: 665
Period size: 221 Copynumber: 1.9 Consensus size: 216
2541910 AATTCAAGAT
*
2541920 GATATTTGGCAATTTGGTTAAACGAGAAATCGAAACCCAGCACATTAGGGCACGTTCCTCGAATT
1 GATATTTAGCAATTTGGTTAAACGAGAAATCGAAACCCAGCACATTAGGGCACGTTCCTCGAATT
* *
2541985 TCCAAACGCAAAACATTACCTTGTTTTGAAATTTTTGGAAGGATATTTAGCTATTTGGTTGAACA
66 TCCAAACGCAAAACATTACCTTATTTTGAAATTTTTGAAAGGATATTTAGCTATTTGGTTGAACA
2542050 AGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTCCCAAACGTAAAACATTGCCT
131 AGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTCCCAAACGTAAAACATTGCCT
2542115 TATTTTGAAATTTTTTAAAAA
196 TATTTTGAAATTTTTTAAAAA
* * *
2542136 GATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
1 GATATTTAGCAATTTGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGGCACG-TTCCTCGA
* *
2542201 ATTTCCAAACGCAAAATATTACCTTATTTTGAAATTTTTTTTAAAGGATATTTAGCTATTTGGTT
63 ATTTCCAAACGCAAAACATTACCTTATTTTGAAA--TTTTTGAAAGGATATTTAGCTATTTGGTT
** * * * *
2542266 GAATGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTTGAATTTCCAAATGTAAAATAT
126 GAACAAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTCCCAAACGTAAAACAT
2542331 TGCCTTA
191 TGCCTTA
2542338 ATTAGAAACA
Statistics
Matches: 183, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
216 23 0.13
218 28 0.15
219 39 0.21
221 93 0.51
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (216 bp):
GATATTTAGCAATTTGGTTAAACGAGAAATCGAAACCCAGCACATTAGGGCACGTTCCTCGAATT
TCCAAACGCAAAACATTACCTTATTTTGAAATTTTTGAAAGGATATTTAGCTATTTGGTTGAACA
AGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTCCCAAACGTAAAACATTGCCT
TATTTTGAAATTTTTTAAAAA
Found at i:2542337 original size:111 final size:110
Alignment explanation
Indices: 2541920--2542320 Score: 621
Period size: 110 Copynumber: 3.7 Consensus size: 110
2541910 AATTCAAGAT
* * * *
2541920 GATATTTGGCAATTTGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGGCACG-TTCCTCGA
1 GATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
* **
2541982 ATTTCCAAACGCAAAACATTACCTTGTTTTGAAA-TTTTTGGAAG
66 ATTTCCAAACGCAAAACATTACCTTATTTTGAAATTTTTTAAAAG
*
2542026 GATATTTAGCTATTTGGTTGAACAAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
1 GATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
* * * *
2542091 ATTCCCAAACGTAAAACATTGCCTTATTTTGAAATTTTTTAAAAA
66 ATTTCCAAACGCAAAACATTACCTTATTTTGAAATTTTTTAAAAG
2542136 GATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
1 GATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
* *
2542201 ATTTCCAAACGCAAAATATTACCTTATTTTGAAATTTTTTTTAAAG
66 ATTTCCAAACGCAAAACATTACCTTATTTTGAAA-TTTTTTAAAAG
* *
2542247 GATATTTAGCTATTTGGTTGAATGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTTGA
1 GATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
2542312 ATTTCCAAA
66 ATTTCCAAA
2542321 TGTAAAATAT
Statistics
Matches: 269, Mismatches: 21, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
106 22 0.08
108 28 0.10
109 37 0.14
110 101 0.38
111 81 0.30
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (110 bp):
GATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
ATTTCCAAACGCAAAACATTACCTTATTTTGAAATTTTTTAAAAG
Found at i:2542404 original size:20 final size:20
Alignment explanation
Indices: 2542379--2542417 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2542369 ATTTATATGC
2542379 ATAATG-GAATAATAAATAAA
1 ATAATGTGAATAA-AAATAAA
*
2542399 ATAATGTGACTAAAAATAA
1 ATAATGTGAATAAAAATAA
2542418 TATGGGCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.26
Consensus pattern (20 bp):
ATAATGTGAATAAAAATAAA
Found at i:2542544 original size:39 final size:39
Alignment explanation
Indices: 2542445--2542544 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 39
2542435 TAATAGATAA
* *
2542445 AAAAGAAAAAATATCAAATAAATAAATAAATAAACTAAGAC
1 AAAA-AAAAAATAAC-AATAAATAAATAAATAAACTAACAC
* *
2542486 --ATAAAAAATGGACATATAAATAAATAAATAAA-TGAACAC
1 AAAAAAAAAAT-AACA-ATAAATAAATAAATAAACT-AACAC
2542525 AAAAAAAAAATAACAATAAA
1 AAAAAAAAAATAACAATAAA
2542545 GGAAAATAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
38 9 0.19
39 28 0.58
40 3 0.06
41 8 0.17
ACGTcount: A:0.71, C:0.07, G:0.05, T:0.17
Consensus pattern (39 bp):
AAAAAAAAAATAACAATAAATAAATAAATAAACTAACAC
Found at i:2542649 original size:30 final size:30
Alignment explanation
Indices: 2542613--2542672 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2542603 ATATGTATGT
2542613 ATATATACA-TAAAATTATGAAAATATAAAA
1 ATATATACATTAAAATTAT-AAAATATAAAA
* * *
2542643 ATATATATATTAAGATTATTAAATATAAAA
1 ATATATACATTAAAATTATAAAATATAAAA
2542673 GTTTATGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (30 bp):
ATATATACATTAAAATTATAAAATATAAAA
Found at i:2543687 original size:14 final size:14
Alignment explanation
Indices: 2543668--2543695 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2543658 GCCAAAAGCT
2543668 CCGTAGCGCCTCCG
1 CCGTAGCGCCTCCG
2543682 CCGTAGCGCCTCCG
1 CCGTAGCGCCTCCG
2543696 TGGGTGGCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.50, G:0.29, T:0.14
Consensus pattern (14 bp):
CCGTAGCGCCTCCG
Found at i:2545804 original size:19 final size:19
Alignment explanation
Indices: 2545767--2545804 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2545757 CTACCTTTCT
*
2545767 TCTTTCTCTTCTCATCCTC
1 TCTTTCTCATCTCATCCTC
2545786 TCTTTCTCAATCTCA-CCTC
1 TCTTTCTC-ATCTCATCCTC
2545805 CCCAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.11, C:0.42, G:0.00, T:0.47
Consensus pattern (19 bp):
TCTTTCTCATCTCATCCTC
Found at i:2546225 original size:154 final size:154
Alignment explanation
Indices: 2546058--2546341 Score: 532
Period size: 154 Copynumber: 1.8 Consensus size: 154
2546048 AATATTATAA
2546058 AACATAAAAATATTAAAATTAAATAATAATATAGAAATGAAATTTTTTTCTCCAAATTTCTCATC
1 AACATAAAAATATTAAAATTAAATAATAATATAGAAATGAAATTTTTTTCTCCAAATTTCTCATC
*
2546123 CAAATATAGTCTAAAAAAGCTTGAAAGCTGAAATTTAAAAATATTTCTATCAAAAGTGAACAATT
66 CAAATACAGTCTAAAAAAGCTTGAAAGCTGAAATTTAAAAATATTTCTATCAAAAGTGAACAATT
2546188 ATATATTGTATCATCAAAATTTTC
131 ATATATTGTATCATCAAAATTTTC
* *
2546212 AACATGAAAATATTAAAATTAAATAATAATATAGAAATGGAATTTTTTTCTCCAAATTTCTCATC
1 AACATAAAAATATTAAAATTAAATAATAATATAGAAATGAAATTTTTTTCTCCAAATTTCTCATC
*
2546277 CAAATACAGTCTAAGAAAGCTTGAAAGCTGAAATTTAAAAATATTTCTATCAAAAGTGAACAATT
66 CAAATACAGTCTAAAAAAGCTTGAAAGCTGAAATTTAAAAATATTTCTATCAAAAGTGAACAATT
2546342 TCTCATCAAA
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
154 126 1.00
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (154 bp):
AACATAAAAATATTAAAATTAAATAATAATATAGAAATGAAATTTTTTTCTCCAAATTTCTCATC
CAAATACAGTCTAAAAAAGCTTGAAAGCTGAAATTTAAAAATATTTCTATCAAAAGTGAACAATT
ATATATTGTATCATCAAAATTTTC
Found at i:2550287 original size:41 final size:41
Alignment explanation
Indices: 2550230--2550574 Score: 555
Period size: 41 Copynumber: 8.4 Consensus size: 41
2550220 GGTTTTAAAA
*
2550230 CCTAGCAGGCTAAGTGCCGGTGAACTGAATAAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
*
2550271 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
*
2550312 CCTAGCAGGCTAAGTGCCGGTGAACTGAATAAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
* *
2550353 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
*
2550394 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCGGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
* * * *
2550435 CCTAGCAGGTTAAGTGCCGGTGATCTGAATTAAGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
2550476 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
* * * *
2550517 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTTTAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
*
2550558 CCTAACAGGCTAAGTGC
1 CCTAGCAGGCTAAGTGC
2550575 TAGTGAATCT
Statistics
Matches: 280, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 280 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.22
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
Found at i:2565904 original size:21 final size:21
Alignment explanation
Indices: 2565878--2565918 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2565868 AGACGAGCAA
* *
2565878 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2565899 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2565919 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:2575070 original size:28 final size:28
Alignment explanation
Indices: 2575019--2575075 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
2575009 TGGAATGAGC
*
2575019 CACTTAAAAAATTATTTATAGAAATAGGT
1 CACTTAAAAAATTATTTACAGAAAT-GGT
*
2575048 CACTTAAAAAA-TATTTACCGAAATGGT
1 CACTTAAAAAATTATTTACAGAAATGGT
2575075 C
1 C
2575076 CAAAAAACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 4 0.15
28 11 0.42
29 11 0.42
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.32
Consensus pattern (28 bp):
CACTTAAAAAATTATTTACAGAAATGGT
Found at i:2576813 original size:47 final size:47
Alignment explanation
Indices: 2576744--2576841 Score: 196
Period size: 47 Copynumber: 2.1 Consensus size: 47
2576734 ATTATTCGAG
2576744 TTATTCAAATTTTAAAATTTAACTCGAAGCTTGACTTATAAATATTT
1 TTATTCAAATTTTAAAATTTAACTCGAAGCTTGACTTATAAATATTT
2576791 TTATTCAAATTTTAAAATTTAACTCGAAGCTTGACTTATAAATATTT
1 TTATTCAAATTTTAAAATTTAACTCGAAGCTTGACTTATAAATATTT
2576838 TTAT
1 TTAT
2576842 GTTTTATATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (47 bp):
TTATTCAAATTTTAAAATTTAACTCGAAGCTTGACTTATAAATATTT
Found at i:2577270 original size:20 final size:21
Alignment explanation
Indices: 2577232--2577274 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
2577222 TTAAAAAAAA
*
2577232 TTTATACTATTTTTTATAATT
1 TTTATACTATTTTTAATAATT
2577253 TTTATACT-TTTTTAATAATT
1 TTTATACTATTTTTAATAATT
2577273 TT
1 TT
2577275 AATTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTATACTATTTTTAATAATT
Found at i:2580573 original size:44 final size:44
Alignment explanation
Indices: 2580507--2580594 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
2580497 TAAAAAAAAT
* * *
2580507 CAATTCTCTTATTGTAAAACATTTATAAGAATTTATTCAAGGGA
1 CAATTCTATCATTGTAAAACATTTAAAAGAATTTATTCAAGGGA
* *
2580551 CAATTCTATCATTGTAAGACATTTAAAAGAATTTATTTAAGGGA
1 CAATTCTATCATTGTAAAACATTTAAAAGAATTTATTCAAGGGA
2580595 AAGGATGGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (44 bp):
CAATTCTATCATTGTAAAACATTTAAAAGAATTTATTCAAGGGA
Found at i:2581991 original size:64 final size:64
Alignment explanation
Indices: 2581901--2582029 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
2581891 AACAAAATGG
2581901 TAGCTTCTTTAGGAACAGAAAGGAACAAGATTTTGATACCCAATGAAGAGAAACAAAGATGAAA
1 TAGCTTCTTTAGGAACAGAAAGGAACAAGATTTTGATACCCAATGAAGAGAAACAAAGATGAAA
*
2581965 TAGCTTCTTTAGGAACAGAAATGAACAAGATTTTGATACCCAATGAAGAGAAACAAAGATGAAA
1 TAGCTTCTTTAGGAACAGAAAGGAACAAGATTTTGATACCCAATGAAGAGAAACAAAGATGAAA
2582029 T
1 T
2582030 CTTTCTAAGA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (64 bp):
TAGCTTCTTTAGGAACAGAAAGGAACAAGATTTTGATACCCAATGAAGAGAAACAAAGATGAAA
Found at i:2583306 original size:20 final size:20
Alignment explanation
Indices: 2583281--2583318 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2583271 TATATTTAAT
2583281 AATATAAAACATAAAAATTA
1 AATATAAAACATAAAAATTA
2583301 AATATAAAACATAAAAAT
1 AATATAAAACATAAAAAT
2583319 ATTTAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (20 bp):
AATATAAAACATAAAAATTA
Found at i:2583353 original size:28 final size:28
Alignment explanation
Indices: 2583286--2583353 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
2583276 TTAATAATAT
* *
2583286 AAAACATAAAAATTAAATATAAAACATA
1 AAAATATATAAATTAAATATAAAACATA
* *
2583314 AAAATATTTAAATTAAATA-AAAA-TTAA
1 AAAATATATAAATTAAATATAAAACAT-A
2583341 AAAATAATATAAA
1 AAAAT-ATATAAA
2583354 AATGAAAGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
26 1 0.03
27 10 0.30
28 22 0.67
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (28 bp):
AAAATATATAAATTAAATATAAAACATA
Found at i:2591286 original size:19 final size:19
Alignment explanation
Indices: 2591261--2591313 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
2591251 AAATTATACT
*
2591261 ATTTTTTTAT-ATTTTTTA
1 ATTTTTTTATAATTTATTA
2591279 ATTTTTTTATAATTTATTA
1 ATTTTTTTATAATTTATTA
*
2591298 CTTTTTTTAATAATTT
1 ATTTTTTT-ATAATTT
2591314 TATTTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.32
19 14 0.45
20 7 0.23
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTTTTTTATAATTTATTA
Found at i:2591303 original size:20 final size:20
Alignment explanation
Indices: 2591257--2591313 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
2591247 AAAAAAATTA
*
2591257 TACTATTTTTTTAT-ATTTTT
1 TACT-TTTTTTTATAATTTAT
*
2591277 TA-ATTTTTTTATAATTTAT
1 TACTTTTTTTTATAATTTAT
*
2591296 TACTTTTTTTAATAATTT
1 TACTTTTTTTTATAATTT
2591314 TATTTTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 9 0.29
19 7 0.23
20 15 0.48
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (20 bp):
TACTTTTTTTTATAATTTAT
Found at i:2593795 original size:29 final size:30
Alignment explanation
Indices: 2593736--2593795 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
2593726 CATATTTCAG
* * *
2593736 GAGCCACATAGGTTGGACACACGACCGTGT
1 GAGCCACACAGGCTGGACACACGACCATGT
2593766 GAGCCACACAGGCTGG-CACAC-AGCCATGT
1 GAGCCACACAGGCTGGACACACGA-CCATGT
2593795 G
1 G
2593796 CCAGACCGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 1 0.04
29 11 0.42
30 14 0.54
ACGTcount: A:0.27, C:0.30, G:0.30, T:0.13
Consensus pattern (30 bp):
GAGCCACACAGGCTGGACACACGACCATGT
Found at i:2594055 original size:18 final size:18
Alignment explanation
Indices: 2594032--2594067 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2594022 GTTTCTTTAT
2594032 CTAATCTTATAGTTATAC
1 CTAATCTTATAGTTATAC
2594050 CTAATCTTATAGTTATAC
1 CTAATCTTATAGTTATAC
2594068 TGACTTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (18 bp):
CTAATCTTATAGTTATAC
Found at i:2606536 original size:18 final size:18
Alignment explanation
Indices: 2606513--2606550 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2606503 AGGTTTATAT
2606513 AATTAGATAAGTTAAAAA
1 AATTAGATAAGTTAAAAA
2606531 AATTAGATAAGTTAAAAA
1 AATTAGATAAGTTAAAAA
2606549 AA
1 AA
2606551 AACACACACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (18 bp):
AATTAGATAAGTTAAAAA
Found at i:2609835 original size:12 final size:12
Alignment explanation
Indices: 2609820--2609857 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2609810 TTCAAAAATA
*
2609820 AAAAAAAATTTT
1 AAAAAATATTTT
*
2609832 AAAAAATGTTTT
1 AAAAAATATTTT
2609844 -AAAAATATTTT
1 AAAAAATATTTT
2609855 AAA
1 AAA
2609858 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (12 bp):
AAAAAATATTTT
Found at i:2610226 original size:18 final size:18
Alignment explanation
Indices: 2610196--2610253 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
2610186 ATAAATGATT
2610196 TTTTATAAA-TATTTTTAA
1 TTTTA-AAATTATTTTTAA
*
2610214 TTTTAAAATTATTTTTTAT
1 TTTTAAAATTA-TTTTTAA
*
2610233 TTTTGAAAATTATTTTAAA
1 TTTT-AAAATTATTTTTAA
2610252 TT
1 TT
2610254 ATTTTGTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 3 0.09
18 7 0.21
19 17 0.50
20 7 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTAAAATTATTTTTAA
Found at i:2610230 original size:20 final size:20
Alignment explanation
Indices: 2610207--2610248 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2610197 TTTATAAATA
2610207 TTTTTAATTTT-AAAATTAT
1 TTTTTAATTTTGAAAATTAT
*
2610226 TTTTTATTTTTGAAAATTAT
1 TTTTTAATTTTGAAAATTAT
2610246 TTT
1 TTT
2610249 AAATTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTTAATTTTGAAAATTAT
Found at i:2616210 original size:50 final size:50
Alignment explanation
Indices: 2616081--2616329 Score: 266
Period size: 50 Copynumber: 4.8 Consensus size: 50
2616071 GATAATAACA
* * ** * *
2616081 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* * *
2616132 TGCCCATGCCATGTCCCAGACATAGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * * *
2616182 TGCCAACGCCATGCCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
2616232 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
2616287 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
2616330 TTACCCAAAT
Statistics
Matches: 166, Mismatches: 25, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 89 0.54
51 32 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:2616260 original size:100 final size:104
Alignment explanation
Indices: 2616080--2616329 Score: 339
Period size: 100 Copynumber: 2.4 Consensus size: 104
2616070 TGATAATAAC
**
2616080 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
2616145 TCCCAGACATAGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATAGTCTTACAGGGGACCTCTCAATCTTAAGG
* * *
2616182 -TGCCAACGCCATGCCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
*
2616245 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATAGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
2616287 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
2616330 TTACCCAAAT
Statistics
Matches: 130, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
99 1 0.01
100 49 0.38
101 35 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 39 0.30
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATAGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:2616445 original size:13 final size:13
Alignment explanation
Indices: 2616424--2616468 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
2616414 GCTTGGATCA
*
2616424 TCATCAAATAAAT
1 TCATAAAATAAAT
2616437 TCATAAAATAAAT
1 TCATAAAATAAAT
2616450 TCATAAAATAAAT
1 TCATAAAATAAAT
2616463 TCATAA
1 TCATAA
2616469 TTTCTGGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:2617980 original size:19 final size:18
Alignment explanation
Indices: 2617936--2617985 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
2617926 ATAAATGAAT
2617936 TTTTATAAA-TATTTTTAA
1 TTTTA-AAACTATTTTTAA
* *
2617954 TTTTAAAATTATTTTTAT
1 TTTTAAAACTATTTTTAA
2617972 TTTTGAAAACTATT
1 TTTT-AAAACTATT
2617986 ATGAATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 3 0.11
18 17 0.61
19 8 0.29
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTAAAACTATTTTTAA
Found at i:2618812 original size:26 final size:26
Alignment explanation
Indices: 2618766--2618815 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2618756 TTAATTATAA
*
2618766 TAATTAAAAATATATTATATAAAAAC
1 TAATTAAAAATATAATATATAAAAAC
*
2618792 TAATTAAAAAT-TAAATGTATAAAA
1 TAATTAAAAATAT-AATATATAAAA
2618816 TCACATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
TAATTAAAAATATAATATATAAAAAC
Found at i:2625884 original size:29 final size:29
Alignment explanation
Indices: 2625850--2625907 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
2625840 TTAAAATTTT
* * *
2625850 TTTAATAGTATAAGGATTAAATTGATCTA
1 TTTAATAATAAAAGGACTAAATTGATCTA
*
2625879 TTTAATAATAAAAGGACTAATTTGATCTA
1 TTTAATAATAAAAGGACTAAATTGATCTA
2625908 ATTCGTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (29 bp):
TTTAATAATAAAAGGACTAAATTGATCTA
Found at i:2634086 original size:15 final size:16
Alignment explanation
Indices: 2634068--2634109 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
2634058 TCGCCCACAT
2634068 AGTTCGCATCAT-ATG
1 AGTTCGCATCATGATG
*
2634083 AGTTCGCA-CGTGATG
1 AGTTCGCATCATGATG
*
2634098 GGTTCGCATCAT
1 AGTTCGCATCAT
2634110 CATGCAACCG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 2 0.09
15 18 0.82
16 2 0.09
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (16 bp):
AGTTCGCATCATGATG
Found at i:2635537 original size:27 final size:27
Alignment explanation
Indices: 2635503--2635567 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
2635493 AATTTATAAA
2635503 ATGAATGTTTA-GATTTTAATAATTTTT
1 ATGAATGTTTATGATTTT-ATAATTTTT
** * *
2635530 ATTTATGTTTATTATTTTTTAATTTTT
1 ATGAATGTTTATGATTTTATAATTTTT
2635557 ATGAATGTTTA
1 ATGAATGTTTA
2635568 AAATTTTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 26 0.84
28 5 0.16
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (27 bp):
ATGAATGTTTATGATTTTATAATTTTT
Found at i:2635573 original size:27 final size:27
Alignment explanation
Indices: 2635503--2635575 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
2635493 AATTTATAAA
* *
2635503 ATGAATGTTT-AGATTTTAATAATTTTT
1 ATGAATGTTTAAAATTTT-TTAATTTTT
** **
2635530 ATTTATGTTTATTATTTTTTAATTTTT
1 ATGAATGTTTAAAATTTTTTAATTTTT
2635557 ATGAATGTTTAAAATTTTT
1 ATGAATGTTTAAAATTTTT
2635576 AATGAGTTCT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
27 31 0.86
28 5 0.14
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (27 bp):
ATGAATGTTTAAAATTTTTTAATTTTT
Found at i:2635766 original size:28 final size:30
Alignment explanation
Indices: 2635711--2635776 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
2635701 TTCATATTTT
2635711 AAATAATTTTAATGATTTTAAATTTTT-AA
1 AAATAATTTTAATGATTTTAAATTTTTAAA
* * *
2635740 AAATAATTTTTAT-TTTTTTAATTTTTAAA
1 AAATAATTTTAATGATTTTAAATTTTTAAA
2635769 AAATAATT
1 AAATAATT
2635777 AAATACTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 11 0.33
29 22 0.67
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (30 bp):
AAATAATTTTAATGATTTTAAATTTTTAAA
Found at i:2638005 original size:29 final size:30
Alignment explanation
Indices: 2637955--2638028 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 30
2637945 TAAACCTCTT
**
2637955 CACTTTCCTCCCAAAACTTTTACT-CCCTCC
1 CACTTTCC-CCCTTAACTTTTACTCCCCTCC
2637985 CACTTTCCCCCTTAACTTTTACTCCCCTCC
1 CACTTTCCCCCTTAACTTTTACTCCCCTCC
*
2638015 CATCTTACCCCCTT
1 CA-CTTTCCCCCTT
2638029 CTACCCCAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 13 0.33
30 16 0.41
31 10 0.26
ACGTcount: A:0.16, C:0.49, G:0.00, T:0.35
Consensus pattern (30 bp):
CACTTTCCCCCTTAACTTTTACTCCCCTCC
Found at i:2653773 original size:11 final size:11
Alignment explanation
Indices: 2653759--2653784 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2653749 TATTATTTAA
2653759 TTATAAAATAT
1 TTATAAAATAT
2653770 TTATAAAATAT
1 TTATAAAATAT
2653781 TTAT
1 TTAT
2653785 TTGATTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTATAAAATAT
Found at i:2669583 original size:12 final size:12
Alignment explanation
Indices: 2669566--2669602 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
2669556 CGAACTAGAG
2669566 TACCCTTATGTT
1 TACCCTTATGTT
2669578 TACCCTTATGTT
1 TACCCTTATGTT
2669590 TACCCTTATGTT
1 TACCCTTATGTT
2669602 T
1 T
2669603 TACTTGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.51
Consensus pattern (12 bp):
TACCCTTATGTT
Found at i:2676318 original size:9 final size:9
Alignment explanation
Indices: 2676296--2676325 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2676286 AGGAATAGTG
2676296 TTTATTTA-
1 TTTATTTAT
2676304 TTTATTTAT
1 TTTATTTAT
2676313 TTTATTTAT
1 TTTATTTAT
2676322 TTTA
1 TTTA
2676326 AATTCACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTAT
Found at i:2676494 original size:21 final size:20
Alignment explanation
Indices: 2676468--2676527 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 20
2676458 AGTAATCTAT
2676468 TAAATGAGTCTTGAATAAATA
1 TAAATGAGT-TTGAATAAATA
*
2676489 TAAATGAGTTTGTTTATAAATA
1 TAAATGAGTTTG--AATAAATA
2676511 TAAATG-GTTTGAATAAA
1 TAAATGAGTTTGAATAAA
2676528 ATTTGTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 5 0.14
20 3 0.09
21 14 0.40
22 13 0.37
ACGTcount: A:0.45, C:0.02, G:0.15, T:0.38
Consensus pattern (20 bp):
TAAATGAGTTTGAATAAATA
Found at i:2682196 original size:20 final size:20
Alignment explanation
Indices: 2682171--2682211 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2682161 AATTTCGTTG
*
2682171 GGTTAAATTCGATTAATTGT
1 GGTTAAATTCAATTAATTGT
2682191 GGTTAAATTCAATTAATTGT
1 GGTTAAATTCAATTAATTGT
2682211 G
1 G
2682212 TTGAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.44
Consensus pattern (20 bp):
GGTTAAATTCAATTAATTGT
Done.