Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 118 of 206
Found at i:35117118 original size:43 final size:43
Alignment explanation
Indices: 35117068--35117333 Score: 345
Period size: 43 Copynumber: 6.2 Consensus size: 43
35117058 AATATTGCAG
* *
35117068 ATCTTATCTTCCCCATGAGTAGGGAAACAGATCTAAGCGGCGA
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGACGA
* * *
35117111 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCCAAGCTATGA
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGACGA
* *
35117154 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCCAAGCTACGA
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGACGA
*
35117197 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGC-ATGA
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGACGA
* * * * * *
35117239 ATCTTAACTTCCCCAAGAGTAGGGAAATAGATCGAGGACGGCGA
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAG-CGACGA
* * * *
35117283 ATCTTATCTTCCCCAAGAGTAGGGAAGCAGATTTAAGCCACGA
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGACGA
*
35117326 GTCTTATC
1 ATCTTATC
35117334 CCGCTGAAGT
Statistics
Matches: 197, Mismatches: 24, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
42 35 0.18
43 129 0.65
44 33 0.17
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (43 bp):
ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGACGA
Found at i:35117601 original size:45 final size:44
Alignment explanation
Indices: 35117552--35117657 Score: 113
Period size: 45 Copynumber: 2.4 Consensus size: 44
35117542 CTTATCCCGA
* *
35117552 CTGAAGTTGCAGTGGGGCAGATCGAAGATGACCAATCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATCGAAGATGA-CAATCCTATCTCC
* * * * * *
35117597 CTGAAGTTACTGTGGAGCAGATTGAAGCTGATATTCCTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATCGAAGATGACAATCCTATCTCC
* *
35117641 CTAAAGTTGTAGTGGAG
1 CTGAAGTTGCAGTGGAG
35117658 TGGATTAAAA
Statistics
Matches: 49, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
44 23 0.47
45 26 0.53
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAGCAGATCGAAGATGACAATCCTATCTCC
Found at i:35120181 original size:14 final size:14
Alignment explanation
Indices: 35120162--35120192 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
35120152 ATATATGTGA
35120162 TTAACTTTAAACAT
1 TTAACTTTAAACAT
35120176 TTAACTTTAAACAT
1 TTAACTTTAAACAT
35120190 TTA
1 TTA
35120193 TATATTACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAACTTTAAACAT
Found at i:35124739 original size:15 final size:15
Alignment explanation
Indices: 35124719--35124761 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
35124709 AACAACTATG
35124719 GAAAAAATGGGAAAA
1 GAAAAAATGGGAAAA
*
35124734 GAAAAAATAGAGAAAA
1 GAAAAAAT-GGGAAAA
*
35124750 -AAAACATGGGAA
1 GAAAAAATGGGAA
35124762 CAATGGGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 4 0.17
15 14 0.58
16 6 0.25
ACGTcount: A:0.67, C:0.02, G:0.23, T:0.07
Consensus pattern (15 bp):
GAAAAAATGGGAAAA
Found at i:35126464 original size:16 final size:16
Alignment explanation
Indices: 35126433--35126469 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
35126423 ATGTGAAGAA
35126433 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
35126449 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
35126465 TATTA
1 TATTA
35126470 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:35126493 original size:18 final size:18
Alignment explanation
Indices: 35126455--35126490 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
35126445 TTATTATTTT
*
35126455 TAAAATTTATTATTAAAA
1 TAAAATTTAATATTAAAA
35126473 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
35126491 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:35126508 original size:16 final size:17
Alignment explanation
Indices: 35126464--35126538 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 17
35126454 TTAAAATTTA
35126464 TTATTAA-AATAA-AAT
1 TTATTAATAATAATAAT
*
35126479 TTA--AATATTAAATAAT
1 TTATTAATAAT-AATAAT
35126495 TTATTAA-AATAATAAAT
1 TTATTAATAATAAT-AAT
35126512 TATATTAATTATATTAATAAT
1 T-TATTAA-TA-A-TAATAAT
35126533 TTATTA
1 TTATTA
35126539 TATGACTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
13 2 0.04
14 2 0.04
15 5 0.11
16 9 0.19
17 6 0.13
18 8 0.17
20 6 0.13
21 5 0.11
22 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATTAATAATAATAAT
Found at i:35126509 original size:34 final size:36
Alignment explanation
Indices: 35126454--35126540 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 36
35126444 ATTATTATTT
*
35126454 TTAA-AATTTATTATTAAAATAAA-AT-TTAA-ATA
1 TTAATAATTTATTATAAAAATAAATATATTAATATA
35126486 TTAAATAATTTATTA-AAATAATAAATTATATTAATTATA
1 TT-AATAATTTATTATAAA-AATAAA-TATATTAA-TATA
35126525 TTAATAATTTATTATA
1 TTAATAATTTATTATA
35126541 TGACTAAATA
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
32 2 0.04
33 4 0.09
34 15 0.33
36 2 0.04
37 4 0.09
38 12 0.27
39 6 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (36 bp):
TTAATAATTTATTATAAAAATAAATATATTAATATA
Found at i:35127227 original size:15 final size:15
Alignment explanation
Indices: 35127207--35127247 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
35127197 CTTGATAAAT
35127207 TGAAAAATTAAATGC
1 TGAAAAATTAAATGC
* *
35127222 TGAAAAAATAAATGT
1 TGAAAAATTAAATGC
35127237 TGAAAAATTAA
1 TGAAAAATTAA
35127248 GTATTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.59, C:0.02, G:0.12, T:0.27
Consensus pattern (15 bp):
TGAAAAATTAAATGC
Found at i:35127747 original size:56 final size:56
Alignment explanation
Indices: 35127676--35127790 Score: 194
Period size: 56 Copynumber: 2.1 Consensus size: 56
35127666 TTTTTTTACT
** *
35127676 TATCTAAATTTGAATTAGCAAATGTGTCTAAAAATATGAATCCGTAAATTATTGAG
1 TATCTAAATCCGAATTAGCAAATGTGTCTAAAAATATGAATCCGTAAACTATTGAG
*
35127732 TATCTAAATCCGAATTAGCAAATGTGTCTAAAAATATGAATCTGTAAACTATTGAG
1 TATCTAAATCCGAATTAGCAAATGTGTCTAAAAATATGAATCCGTAAACTATTGAG
35127788 TAT
1 TAT
35127791 TATTGTGTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (56 bp):
TATCTAAATCCGAATTAGCAAATGTGTCTAAAAATATGAATCCGTAAACTATTGAG
Found at i:35138117 original size:14 final size:14
Alignment explanation
Indices: 35138098--35138124 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35138088 GTGGTCCAGT
35138098 TGAACTGAACCGAG
1 TGAACTGAACCGAG
35138112 TGAACTGAACCGA
1 TGAACTGAACCGA
35138125 CTAGGAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:35138800 original size:22 final size:22
Alignment explanation
Indices: 35138772--35138813 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
35138762 TTAAAATTAT
35138772 CGTACTAAGCTCTCATGTTTCA
1 CGTACTAAGCTCTCATGTTTCA
35138794 CGTACTAAGCTCTCATGTTT
1 CGTACTAAGCTCTCATGTTT
35138814 GAACAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.38
Consensus pattern (22 bp):
CGTACTAAGCTCTCATGTTTCA
Found at i:35144130 original size:30 final size:30
Alignment explanation
Indices: 35144096--35144157 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
35144086 TTAATTATTT
* *
35144096 TTAAAAATTTGGTAACTCTTTTTATAAATA
1 TTAAAAATTAGATAACTCTTTTTATAAATA
** *
35144126 TTAAAAATTAGATGCCTCTTTTTGTAAATA
1 TTAAAAATTAGATAACTCTTTTTATAAATA
35144156 TT
1 TT
35144158 TTCAAAAAGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (30 bp):
TTAAAAATTAGATAACTCTTTTTATAAATA
Found at i:35148254 original size:36 final size:39
Alignment explanation
Indices: 35148214--35148295 Score: 109
Period size: 36 Copynumber: 2.2 Consensus size: 39
35148204 GACTACGAGT
*
35148214 TGATGAGTGTTGGGCAC-ATTTA-TACTT-TGATTATA-C
1 TGATGAGTGTTGGGCACAATTTACTACTTCGGATT-TACC
*
35148250 TGATGAGTGTTGGGCGCAATTTACTACTTCGGATTTACC
1 TGATGAGTGTTGGGCACAATTTACTACTTCGGATTTACC
35148289 TGATGAG
1 TGATGAG
35148296 GCACTGGGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
36 16 0.40
37 5 0.12
38 7 0.17
39 12 0.30
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (39 bp):
TGATGAGTGTTGGGCACAATTTACTACTTCGGATTTACC
Found at i:35150516 original size:136 final size:136
Alignment explanation
Indices: 35150257--35150518 Score: 294
Period size: 136 Copynumber: 1.9 Consensus size: 136
35150247 TCATTAGGGT
* * ** * * *
35150257 TTACCATGTTTCGGGTGTTGGTCTTGAATGTCCTATTGATGGCTGAGTTCTGACATTTGTTGCGG
1 TTACCATGTTTCGGGTGCTGGTCTCGAATGTCCTACCGATGGCTAAGTTCTGAAATTTGTTACGG
* * * * * *
35150322 GTACTCGACAGCTTGTGGAACAGCACCGTATAGCTACATTTCGACTGATAGCTTGTGTGAGTAGA
66 ATAATCGACAGCTTGTGGAACAGCACCGTATAGCTACATTTCGACCGACAACTCGTGTGAGTAGA
35150387 CCCAGG
131 CCCAGG
* * * *
35150393 TTACCATGTTTTGGGTGCTGGTCTCGAATGTCCTACCGGTGGCTAAGTT-TCGAAATTTTTTATG
1 TTACCATGTTTCGGGTGCTGGTCTCGAATGTCCTACCGATGGCTAAGTTCT-GAAATTTGTTACG
* * * * *
35150457 GATAATCGATAGCTTGTGGAGCAGCATCGTGTAGCTAC-GTTCTGACCGACAACTCGTGTGAG
65 GATAATCGACAGCTTGTGGAACAGCACCGTATAGCTACATTTC-GACCGACAACTCGTGTGAG
35150519 CAGGCCCATT
Statistics
Matches: 102, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
135 4 0.04
136 98 0.96
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.33
Consensus pattern (136 bp):
TTACCATGTTTCGGGTGCTGGTCTCGAATGTCCTACCGATGGCTAAGTTCTGAAATTTGTTACGG
ATAATCGACAGCTTGTGGAACAGCACCGTATAGCTACATTTCGACCGACAACTCGTGTGAGTAGA
CCCAGG
Found at i:35155919 original size:15 final size:17
Alignment explanation
Indices: 35155895--35155932 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
35155885 TAAAATATTA
35155895 TTATTAGATT-AAA-AC
1 TTATTAGATTGAAACAC
*
35155910 TTATTTGATTGAAACAC
1 TTATTAGATTGAAACAC
35155927 TTATTA
1 TTATTA
35155933 TTTTGTCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 9 0.47
16 3 0.16
17 7 0.37
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (17 bp):
TTATTAGATTGAAACAC
Found at i:35158384 original size:35 final size:35
Alignment explanation
Indices: 35158327--35158436 Score: 157
Period size: 35 Copynumber: 3.1 Consensus size: 35
35158317 TATCGTTCCA
* * *
35158327 TAGAGCCAATAGACCATTTCTATGATGCCGCTTCG
1 TAGAGCCAGTAGATCATTTCTATGATGCCGCTCCG
* *
35158362 TAGAGCCAGTAGATCATCTCTATGATGCCGCTCCT
1 TAGAGCCAGTAGATCATTTCTATGATGCCGCTCCG
*
35158397 TAGAGCCAGTAGATCATTTCCATGATGCCGCTCCG
1 TAGAGCCAGTAGATCATTTCTATGATGCCGCTCCG
*
35158432 CAGAG
1 TAGAG
35158437 TGAGTAAACT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (35 bp):
TAGAGCCAGTAGATCATTTCTATGATGCCGCTCCG
Found at i:35170620 original size:22 final size:22
Alignment explanation
Indices: 35170592--35170702 Score: 150
Period size: 22 Copynumber: 5.0 Consensus size: 22
35170582 TTTATTGTTC
*
35170592 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
35170614 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
35170636 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
35170658 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
35170680 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
35170702 A
1 A
35170703 GCCTAATATT
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 78 1.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:35176158 original size:44 final size:46
Alignment explanation
Indices: 35176075--35176165 Score: 150
Period size: 44 Copynumber: 2.0 Consensus size: 46
35176065 TTTGCTGTAT
*
35176075 TGGAATAGAGGCATAATAGGTAATTCTTTTGTTTGGTTGAATGGAA
1 TGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTTGAATGGAA
*
35176121 TGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGGAA
1 TGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTTGAATGGAA
35176165 T
1 T
35176166 AGAGATGTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 24 0.56
45 3 0.07
46 16 0.37
ACGTcount: A:0.27, C:0.04, G:0.31, T:0.37
Consensus pattern (46 bp):
TGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTTGAATGGAA
Found at i:35176161 original size:39 final size:44
Alignment explanation
Indices: 35176075--35176169 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 44
35176065 TTTGCTGTAT
*
35176075 TGGAATAGAGGCATAATAGGTAATTCTTTTGTTTGGTTGAATGGAA
1 TGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTT--ATGGAA
*
35176121 TGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T-GAA
1 TGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTTATGGAA
35176160 TGGAATAGAG
1 TGGAATAGAG
35176170 ATGTAATAGC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
39 13 0.28
40 1 0.02
43 1 0.02
44 13 0.28
45 3 0.06
46 16 0.34
ACGTcount: A:0.28, C:0.04, G:0.32, T:0.36
Consensus pattern (44 bp):
TGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTTATGGAA
Found at i:35176347 original size:18 final size:18
Alignment explanation
Indices: 35176324--35176457 Score: 90
Period size: 18 Copynumber: 7.9 Consensus size: 18
35176314 TTATTATTAA
35176324 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
35176342 ATATAATTTAAT-AAAAT
1 ATATAATTTAATAAAAAT
*
35176359 ATATGAATTTACT-AAAAT
1 ATAT-AATTTAATAAAAAT
* * * *
35176377 -CATAATAT-ATAATACT
1 ATATAATTTAATAAAAAT
* * *
35176393 ATAAAATATAATTTAAAAT
1 ATATAATTTAA-TAAAAAT
*
35176412 A-ATAA-TT-AT--TAA-
1 ATATAATTTAATAAAAAT
35176424 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
*
35176442 ATATAATTTGATAAAA
1 ATATAATTTAATAAAA
35176458 TTCTTAGTAT
Statistics
Matches: 89, Mismatches: 16, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
12 1 0.01
13 6 0.07
14 2 0.02
15 4 0.04
16 8 0.09
17 20 0.22
18 43 0.48
19 5 0.06
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:35176384 original size:41 final size:40
Alignment explanation
Indices: 35176339--35176522 Score: 116
Period size: 41 Copynumber: 4.6 Consensus size: 40
35176329 ATTTAATAAA
*
35176339 AATATATAATTTAATAAAATATATGAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATATAT-AATTTAATAAAATCAT
* *
35176380 AATATATAA--TACTATAAA-ATATAATTTAAAATAATAATTATT
1 AATATATAATTTAATA-AAATATATAATTT--AATAA-AATCA-T
* *
35176422 AA-ATATAATTTAATAAAAATATATAATTTGATAAAATTCTT
1 AATATATAATTTAAT-AAAATATATAATTTAATAAAA-TCAT
* * * * *
35176463 AGTAT-TAA-AT-AT-TATTATATGAATTTATTAAAATCAT
1 AATATATAATTTAATAAAATATAT-AATTTAATAAAATCAT
*
35176500 AATATATAATACT-ATAAAATATA
1 AATATATAAT-TTAATAAAATATA
35176523 ATTTAAAATA
Statistics
Matches: 109, Mismatches: 18, Indels: 32
0.69 0.11 0.20
Matches are distributed among these distances:
37 13 0.12
38 18 0.17
39 10 0.09
40 11 0.10
41 31 0.28
42 10 0.09
43 6 0.06
44 10 0.09
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (40 bp):
AATATATAATTTAATAAAATATATAATTTAATAAAATCAT
Found at i:35176418 original size:13 final size:12
Alignment explanation
Indices: 35176394--35176434 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
35176384 TATAATACTA
35176394 TAAAATATAATT
1 TAAAATATAATT
35176406 TAAAATAATAATT
1 TAAAAT-ATAATT
*
35176419 ATTAAATATAATT
1 -TAAAATATAATT
35176432 TAA
1 TAA
35176435 TAAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:35176517 original size:61 final size:61
Alignment explanation
Indices: 35176337--35176540 Score: 196
Period size: 59 Copynumber: 3.4 Consensus size: 61
35176327 TAATTTAATA
*
35176337 AAAATATATAATTT--AATAA-AA-TATATGAATTTACTAAAATCATAATATATAATACTAT
1 AAAAT-TATAATTTAAAATAATAATTATATGAATTTATTAAAATCATAATATATAATACTAT
* * * * * *
35176395 AAAA-TATAATTTAAAATAATAATTAT-TAAATATAATT-TAATAAAAATATATAAT-TTGAT
1 AAAATTATAATTTAAAATAATAATTATATGAAT-TTATTAAAATCATAATATATAATACT-AT
* * *
35176454 AAAATTCTTAGTATT-AAAT-ATTATTATATGAATTTATTAAAATCATAATATATAATACTAT
1 AAAATT-ATAAT-TTAAAATAATAATTATATGAATTTATTAAAATCATAATATATAATACTAT
35176515 AAAA-TATAATTTAAAATAATAATTAT
1 AAAATTATAATTTAAAATAATAATTAT
35176541 TAAATATAAT
Statistics
Matches: 113, Mismatches: 19, Indels: 26
0.72 0.12 0.16
Matches are distributed among these distances:
56 8 0.07
58 12 0.11
59 33 0.29
60 26 0.23
61 31 0.27
62 3 0.03
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (61 bp):
AAAATTATAATTTAAAATAATAATTATATGAATTTATTAAAATCATAATATATAATACTAT
Found at i:35176538 original size:13 final size:12
Alignment explanation
Indices: 35176514--35176553 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
35176504 TATAATACTA
35176514 TAAAATATAATT
1 TAAAATATAATT
35176526 TAAAATAATAATT
1 TAAAAT-ATAATT
*
35176539 ATTAAATATAATT
1 -TAAAATATAATT
35176552 TA
1 TA
35176554 TAATCTACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 7 0.29
13 12 0.50
14 5 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:35179285 original size:15 final size:14
Alignment explanation
Indices: 35179259--35179294 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
35179249 ACCGGTGGGA
35179259 ATAAACAATAAAATG
1 ATAAA-AATAAAATG
35179274 ATGAAAAATAAAATG
1 AT-AAAAATAAAATG
35179289 ATAAAA
1 ATAAAA
35179295 TTAATCATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 13 0.65
16 3 0.15
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.19
Consensus pattern (14 bp):
ATAAAAATAAAATG
Found at i:35179822 original size:10 final size:10
Alignment explanation
Indices: 35179807--35179833 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
35179797 GTAGCATCTA
35179807 TAACAATGCT
1 TAACAATGCT
35179817 TAACAATGCT
1 TAACAATGCT
35179827 TAACAAT
1 TAACAAT
35179834 TAATAAACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (10 bp):
TAACAATGCT
Found at i:35180051 original size:36 final size:36
Alignment explanation
Indices: 35180011--35180083 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
35180001 CTTTTTAATG
35180011 ATAGTTACATGATTAAACTTTCTAAAACCTCATGTT
1 ATAGTTACATGATTAAACTTTCTAAAACCTCATGTT
35180047 ATAGTTACATGATTAAACTTTCTAAAACCTCATGTT
1 ATAGTTACATGATTAAACTTTCTAAAACCTCATGTT
35180083 A
1 A
35180084 AAGGTAAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.38
Consensus pattern (36 bp):
ATAGTTACATGATTAAACTTTCTAAAACCTCATGTT
Found at i:35180921 original size:89 final size:90
Alignment explanation
Indices: 35180786--35181042 Score: 301
Period size: 89 Copynumber: 2.8 Consensus size: 90
35180776 ATTTTTTTTT
*
35180786 AAAAAACAATTAAGCTCTTTCTTTTTTTTTTCACTCAATT-AGGTACTTGAACTTTCAAAATGCA
1 AAAAAACAATTAAGCCCTTTC-TTTTTTTTTCACTCAATTGA-GTACTTGAACTTTCAAAATGCA
35180850 TCAAAAAAG--CTCTCAA-ACTTT-AAAA
64 T-AAAAAAGACCT-TCAATACTTTCAAAA
*
35180875 AAAAAAGCAATTAAGCCCCTTCTTTTTTTTTCACTCAATTGAGTACTTGAACTTTCAAAATGCAT
1 AAAAAA-CAATTAAGCCCTTTCTTTTTTTTTCACTCAATTGAGTACTTGAACTTTCAAAATGCAT
**
35180940 AAAAAAAGACCTTCAATTTTTTTTCAAAA
65 -AAAAAAGACCTTCAA--TACTTTCAAAA
* * * * **
35180969 AAAAAACAATTAAGCCCTTTGTTTTTTCTGCA-TCCAATTGGGTACTTGAACTGCCAAAATGCAT
1 AAAAAACAATTAAGCCCTTTCTTTTTTTTTCACT-CAATTGAGTACTTGAACTTTCAAAATGCAT
35181033 AAAAAAGACC
65 AAAAAAGACC
35181043 CTTTGACCGC
Statistics
Matches: 147, Mismatches: 12, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
89 54 0.37
90 18 0.12
91 2 0.01
92 11 0.07
93 52 0.35
94 10 0.07
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.34
Consensus pattern (90 bp):
AAAAAACAATTAAGCCCTTTCTTTTTTTTTCACTCAATTGAGTACTTGAACTTTCAAAATGCATA
AAAAAGACCTTCAATACTTTCAAAA
Found at i:35181153 original size:9 final size:9
Alignment explanation
Indices: 35181141--35181287 Score: 104
Period size: 10 Copynumber: 15.4 Consensus size: 9
35181131 GCATGTGACA
35181141 AAAAATTAT
1 AAAAATTAT
35181150 AAAAA--AT
1 AAAAATTAT
*
35181157 AAAAATCAGT
1 AAAAATTA-T
*
35181167 AAAATTTAT
1 AAAAATTAT
*
35181176 AAAAATCACT
1 AAAAATTA-T
**
35181186 AAATTTTAAT
1 AAAAATT-AT
*
35181196 AAAAATATAAA
1 AAAAAT-T-AT
35181207 AAAAATT-T
1 AAAAATTAT
35181215 -AAAATTGATT
1 AAAAATT-A-T
35181225 AAAAATTAT
1 AAAAATTAT
35181234 AAAAAATTTAT
1 -AAAAA-TTAT
35181245 AAAAATTAT
1 AAAAATTAT
35181254 AAAAAAATTAT
1 --AAAAATTAT
35181265 AAAAATTAT
1 AAAAATTAT
35181274 AAAAAATTAT
1 -AAAAATTAT
35181284 AAAA
1 AAAA
35181288 TGCATCAAGA
Statistics
Matches: 112, Mismatches: 11, Indels: 30
0.73 0.07 0.20
Matches are distributed among these distances:
7 13 0.12
9 31 0.28
10 39 0.35
11 29 0.26
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:35181206 original size:18 final size:20
Alignment explanation
Indices: 35181154--35181201 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
35181144 AATTATAAAA
*
35181154 AATAAAAATCAGTAAAATTT
1 AATAAAAATCACTAAAATTT
*
35181174 -ATAAAAATCACTAAATTTT
1 AATAAAAATCACTAAAATTT
35181193 AATAAAAAT
1 AATAAAAAT
35181202 ATAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.31
Consensus pattern (20 bp):
AATAAAAATCACTAAAATTT
Found at i:35181549 original size:9 final size:9
Alignment explanation
Indices: 35181529--35181638 Score: 78
Period size: 9 Copynumber: 11.6 Consensus size: 9
35181519 TTATTATGAC
35181529 TTTATAAAAT
1 TTTAT-AAAT
35181539 TTTATAAATT
1 TTTATAAA-T
* *
35181549 TTTTTATAT
1 TTTATAAAT
35181558 TTTATAAATT
1 TTTATAAA-T
*
35181568 TCTTACAAAT
1 T-TTATAAAT
*
35181578 TTTATAATT
1 TTTATAAAT
*
35181587 TTTAATATAT
1 TTT-ATAAAT
*
35181597 TTTAT-ATT
1 TTTATAAAT
35181605 TTTATTAAAAT
1 TTTA-T-AAAT
* *
35181616 TTAATAATT
1 TTTATAAAT
35181625 TTTATAAAT
1 TTTATAAAT
35181634 TTTAT
1 TTTAT
35181639 TGATTTTTAT
Statistics
Matches: 77, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
8 5 0.06
9 37 0.48
10 24 0.31
11 11 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTATAAAT
Found at i:35181561 original size:19 final size:19
Alignment explanation
Indices: 35181537--35181648 Score: 88
Period size: 19 Copynumber: 5.9 Consensus size: 19
35181527 ACTTTATAAA
*
35181537 ATTTTATAAATTTTTTTAT
1 ATTTTATAAATTTTTATAT
* *
35181556 ATTTTATAAATTTCTTACAA
1 ATTTTATAAATTT-TTATAT
35181576 ATTTTAT-AATTTTTAATAT
1 ATTTTATAAATTTTT-ATAT
*
35181595 ATTTTAT--ATTTTTATTAA
1 ATTTTATAAATTTTTA-TAT
* *
35181613 AATTTA-ATAATTTTTATAA
1 ATTTTATA-AATTTTTATAT
**
35181632 ATTTTATTGATTTTTAT
1 ATTTTATAAATTTTTAT
35181649 TTTTATCATT
Statistics
Matches: 76, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
17 1 0.01
18 15 0.20
19 43 0.57
20 17 0.22
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.62
Consensus pattern (19 bp):
ATTTTATAAATTTTTATAT
Found at i:35181578 original size:39 final size:37
Alignment explanation
Indices: 35181529--35181638 Score: 132
Period size: 39 Copynumber: 2.9 Consensus size: 37
35181519 TTATTATGAC
*
35181529 TTTA-TAAAATTTTATAAATTTTTTTATATTTTATAAA
1 TTTATTAAAATTTTAT-AATTTTTATATATTTTATAAA
* **
35181566 TTTCTTACAAATTTTATAATTTTTAATATATTTTATATT
1 TTTATTA-AAATTTTATAATTTTT-ATATATTTTATAAA
* *
35181605 TTTATTAAAATTTAATAATTTTTATAAATTTTAT
1 TTTATTAAAATTTTATAATTTTTATATATTTTAT
35181639 TGATTTTTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
37 13 0.21
38 24 0.38
39 26 0.41
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (37 bp):
TTTATTAAAATTTTATAATTTTTATATATTTTATAAA
Found at i:35181589 original size:29 final size:29
Alignment explanation
Indices: 35181529--35181590 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
35181519 TTATTATGAC
* * *
35181529 TTTATAAAATTTTATAAATTTTTTTATAT
1 TTTATAAAATTTTACAAATTTTATAATAT
*
35181558 TTTATAAATTTCTTACAAATTTTATAAT-T
1 TTTATAAAATT-TTACAAATTTTATAATAT
35181587 TTTA
1 TTTA
35181591 ATATATTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTATAAAATTTTACAAATTTTATAATAT
Found at i:35183324 original size:15 final size:16
Alignment explanation
Indices: 35183306--35183336 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
35183296 ACATATGTAT
35183306 TAGAATAGTTA-AACA
1 TAGAATAGTTAGAACA
35183321 TAGAATAGTTAGAACA
1 TAGAATAGTTAGAACA
35183337 ACTTTAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (16 bp):
TAGAATAGTTAGAACA
Found at i:35186716 original size:27 final size:27
Alignment explanation
Indices: 35186657--35186717 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
35186647 TTTTGGCCTC
**
35186657 GCAAA-TAAGGGTTTGCCAGTGTTTCA
1 GCAAACTAAGGGTTTGCCAGTACTTCA
* *
35186683 TCGAACTAAGGGTTTGCCAGTACTTCA
1 GCAAACTAAGGGTTTGCCAGTACTTCA
35186710 GCAAACTA
1 GCAAACTA
35186718 GGGAATTCAC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (27 bp):
GCAAACTAAGGGTTTGCCAGTACTTCA
Found at i:35186859 original size:28 final size:28
Alignment explanation
Indices: 35186823--35186909 Score: 95
Period size: 28 Copynumber: 3.1 Consensus size: 28
35186813 CGTAAGTTGA
35186823 GTTCGCTAGTCTGTTTGGCAAACTGAGG
1 GTTCGCTAGTCTGTTTGGCAAACTGAGG
* ** * *
35186851 GTTCACTAG-CATGTTTGGTGAATTGGGG
1 GTTCGCTAGTC-TGTTTGGCAAACTGAGG
* *
35186879 GTTCGCTAGTCTGTTTAGCTAACTGAGG
1 GTTCGCTAGTCTGTTTGGCAAACTGAGG
35186907 GTT
1 GTT
35186910 TGCCAGTTGA
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
27 1 0.02
28 44 0.96
29 1 0.02
ACGTcount: A:0.17, C:0.15, G:0.32, T:0.36
Consensus pattern (28 bp):
GTTCGCTAGTCTGTTTGGCAAACTGAGG
Found at i:35192350 original size:18 final size:18
Alignment explanation
Indices: 35192327--35192362 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35192317 TTTCATAATT
*
35192327 TCACTTTTTCACTTTCAA
1 TCACTTTTCCACTTTCAA
*
35192345 TCACTTTTCCATTTTCAA
1 TCACTTTTCCACTTTCAA
35192363 GTCAATATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.28, G:0.00, T:0.50
Consensus pattern (18 bp):
TCACTTTTCCACTTTCAA
Found at i:35192640 original size:50 final size:50
Alignment explanation
Indices: 35192577--35192863 Score: 290
Period size: 51 Copynumber: 5.7 Consensus size: 50
35192567 TTATTCGATA
* *
35192577 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGATTTACGGTT
* * * *
35192627 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTTTCCGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGA-CCAAGATTTACGGTT
* * * ** *
35192678 CACATAGTAGCCTTCACTTAGTACTACA-ATGTGACCATCATTTATCGATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGATTTA-CGGTT
* * * * *
35192728 CATGTAGTAGCCTTTACACAGTACTACACACGTGACCAAAGCTTCT-CGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAGATT-TACGGTT
* * * * ** *
35192779 CACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGATTTA-CGGTT
*
35192830 CACGTAGTAGCCTTCACACAGTACTACACACGTG
1 CACGTAGTAGCCTTCACATAGTACTACACACGTG
35192864 TTCATCGATA
Statistics
Matches: 187, Mismatches: 43, Indels: 13
0.77 0.18 0.05
Matches are distributed among these distances:
49 6 0.03
50 69 0.37
51 108 0.58
52 3 0.02
53 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGATTTACGGTT
Found at i:35192735 original size:101 final size:102
Alignment explanation
Indices: 35192575--35192863 Score: 431
Period size: 101 Copynumber: 2.9 Consensus size: 102
35192565 AATTATTCGA
* * * * *** *
35192575 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA-CGGTTCACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
* *
35192639 TTCACATAGTACTACACACGTGATCAAAGCTT-TCCGG
66 TTCACACAGTACTACACACGTGACCAAAGCTTCT-CGG
*
35192676 TACACATAGTAGCCTTCACTTAGTACTACA-ATGTGACCATCATTTATCGATTCATGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
*
35192740 TTTACACAGTACTACACACGTGACCAAAGCTTCTCGG
66 TTCACACAGTACTACACACGTGACCAAAGCTTCTCGG
*
35192777 TACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
35192842 TTCACACAGTACTACACACGTG
66 TTCACACAGTACTACACACGTG
35192864 TTCATCGATA
Statistics
Matches: 170, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
100 11 0.06
101 104 0.61
102 55 0.32
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (102 bp):
TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
TTCACACAGTACTACACACGTGACCAAAGCTTCTCGG
Found at i:35198152 original size:23 final size:23
Alignment explanation
Indices: 35198102--35198153 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
35198092 CGATTTTGTT
*
35198102 GAAGCCTTTGTGGCTGTTCTGTG
1 GAAGCCTTTGTGGCTGTTCTGAG
* * * *
35198125 AAAGCGTTTGTGGTTTTTCTGAG
1 GAAGCCTTTGTGGCTGTTCTGAG
35198148 GAAGCC
1 GAAGCC
35198154 CTTTTGATTG
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.15, C:0.15, G:0.33, T:0.37
Consensus pattern (23 bp):
GAAGCCTTTGTGGCTGTTCTGAG
Found at i:35201508 original size:23 final size:23
Alignment explanation
Indices: 35201468--35201519 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
35201458 AAGTTATCGA
* * **
35201468 TTCTGTGGAAGCCTTTGTGGTTG
1 TTCTGAGGAAGCCCTTGTAATTG
*
35201491 TTCTGAGGATGCCCTTGTAATTG
1 TTCTGAGGAAGCCCTTGTAATTG
35201514 TTCTGA
1 TTCTGA
35201520 TATATGAGAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.13, C:0.15, G:0.29, T:0.42
Consensus pattern (23 bp):
TTCTGAGGAAGCCCTTGTAATTG
Found at i:35203215 original size:15 final size:15
Alignment explanation
Indices: 35203172--35203216 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
35203162 CCCTTCTTTT
* *
35203172 TCATCACAAATCACA
1 TCATCACATATCATA
35203187 TCATCACATATCATA
1 TCATCACATATCATA
35203202 TCATCACATATCATA
1 TCATCACATATCATA
35203217 CACAAATGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (15 bp):
TCATCACATATCATA
Found at i:35214564 original size:41 final size:42
Alignment explanation
Indices: 35214510--35214703 Score: 169
Period size: 41 Copynumber: 4.6 Consensus size: 42
35214500 TGAATGTAAG
* *
35214510 GGTTGCTATGTGCTGATTCC-CCGAATCATTTATTATAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCATTTATTATAAGGT
* * * *
35214551 GGTTGCTAAGTGCTTATTCCACCGTATCCTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACCGTATCATTTATTAT--AAGGT
* * * **
35214594 GGTTGCTATGTGATAATTCC-CCGTATCATAAATTATAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCATTTATTATAAGGT
* * ** *
35214635 GGTTGCTAAGTGCTGATTCCACCGGGATCCTTTGAACATAAAGT
1 GGTTGCTAAGTGCTGATTCCACC-GTATCATTT-ATTATAAGGT
* *
35214679 GGTTTCTAAGTGCTGATTCAACCGT
1 GGTTGCTAAGTGCTGATTCCACCGT
35214704 GTAATGGTTA
Statistics
Matches: 120, Mismatches: 26, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
40 4 0.03
41 35 0.29
42 26 0.22
43 23 0.19
44 32 0.27
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCATTTATTATAAGGT
Found at i:35217327 original size:103 final size:104
Alignment explanation
Indices: 35217148--35217413 Score: 426
Period size: 103 Copynumber: 2.6 Consensus size: 104
35217138 TAGCCGTTAT
** * * *
35217148 TGGTGGATCCCGCACTTAACACCACCACTGAATCAGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
35217213 AATCAGCACATAGCAA-CCCCCTTTTTATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCCTTTTCATTTCAAAGATA
*
35217251 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACTCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
35217316 AATCAGCACATAGCAACCCCCCTTTTCATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCCTTTTCATTTCAAAGATA
* * **
35217355 TGGTGGATATCGCACTTAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
35217414 TTTATATACA
Statistics
Matches: 150, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
103 75 0.50
104 75 0.50
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (104 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCCTTTTCATTTCAAAGATA
Found at i:35217389 original size:104 final size:103
Alignment explanation
Indices: 35217148--35217413 Score: 417
Period size: 104 Copynumber: 2.6 Consensus size: 103
35217138 TAGCCGTTAT
** * *
35217148 TGGTGGATCCCGCACTTAACACCA-CCACTGAATCAGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCCA-TGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
*
35217212 GAATCAGCACATAGCAACCCCCTTTTTATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
* *
35217251 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACTCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCCATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
35217316 AATCAGCACATAGCAACCCCCCTTTTCATTTCAAAGATA
66 AATCAGCACATAGCAA-CCCCCTTTTCATTTCAAAGATA
* **
35217355 TGGTGGATATCGCACTTAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGATATCGCACTTAGCACCACCCATGAATCGGGGAATCAGCACTTAGCAACCCCT
35217414 TTTATATACA
Statistics
Matches: 149, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
103 72 0.48
104 77 0.52
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (103 bp):
TGGTGGATATCGCACTTAGCACCACCCATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
Found at i:35217775 original size:29 final size:29
Alignment explanation
Indices: 35217742--35217805 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
35217732 TAATCCACCA
35217742 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
35217771 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
35217801 CCCAA
1 CCCAA
35217806 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:35217779 original size:30 final size:30
Alignment explanation
Indices: 35217749--35217805 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
35217739 CCACCCAACT
35217749 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
35217778 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
35217806 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:35224577 original size:29 final size:29
Alignment explanation
Indices: 35224544--35224607 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
35224534 TAATCCACCA
35224544 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
35224573 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
35224603 CCCAA
1 CCCAA
35224608 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:35224581 original size:30 final size:30
Alignment explanation
Indices: 35224551--35224607 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
35224541 CCACCCAACT
35224551 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
35224580 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
35224608 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:35226896 original size:47 final size:47
Alignment explanation
Indices: 35226779--35226898 Score: 143
Period size: 47 Copynumber: 2.6 Consensus size: 47
35226769 ATTAACGAAA
* * * * * *
35226779 AAGACCATGGTTGGACTATGGCAACATGTGATATGTGATTTCTGTAT
1 AAGACCATAGCTGGGCTATGGCATCATGTGATATGTGACTACTGTAT
* * *
35226826 AAGACCATATCTGGGATATGGCATCAGTGTGATATGTG-CTACTGTGT
1 AAGACCATAGCTGGGCTATGGCATCA-TGTGATATGTGACTACTGTAT
35226873 AAGACCATAGCTGGGCTATGGCATCA
1 AAGACCATAGCTGGGCTATGGCATCA
35226899 ATATGTAAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 50 0.82
48 11 0.18
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (47 bp):
AAGACCATAGCTGGGCTATGGCATCATGTGATATGTGACTACTGTAT
Found at i:35228690 original size:21 final size:20
Alignment explanation
Indices: 35228666--35228715 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
35228656 AATCTATATA
* *
35228666 TATGTATATTTATTTTTCTTT
1 TATGTATATTT-TTTCTCTCT
*
35228687 TATGTACATTTTTTCTCTCT
1 TATGTATATTTTTTCTCTCT
*
35228707 TATATATAT
1 TATGTATAT
35228716 ATATATACGT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.22, C:0.10, G:0.04, T:0.64
Consensus pattern (20 bp):
TATGTATATTTTTTCTCTCT
Found at i:35232486 original size:42 final size:41
Alignment explanation
Indices: 35232365--35232555 Score: 208
Period size: 41 Copynumber: 4.6 Consensus size: 41
35232355 TCTTTGAATG
* * *
35232365 TAAGG-GGTTGCTAAGTG-TAGATTCCCCGAATCATTGATCAA
1 TAAGGTGGTTGCTAAGTGCT-GATTCCCCGTATCCTTGAT-TA
* * *
35232406 AAAGG-GGTTGCTATGTGCTGATTCCCCGTATCATTGATTA
1 TAAGGTGGTTGCTAAGTGCTGATTCCCCGTATCCTTGATTA
* *
35232446 TAAGGTGGTTGCTAAGTGCTTATTCTACCGTATCCTTGATTA
1 TAAGGTGGTTGCTAAGTGCTGATTC-CCCGTATCCTTGATTA
* * * * *
35232488 TGAAAGAGGTTGCTATGTGCTAATTCCCCGTATCCTTAATTA
1 T-AAGGTGGTTGCTAAGTGCTGATTCCCCGTATCCTTGATTA
35232530 TAAGGTGGTTGCTAAGTGCTGATTCC
1 TAAGGTGGTTGCTAAGTGCTGATTCC
35232556 ACCATGTAAC
Statistics
Matches: 127, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
40 5 0.04
41 71 0.56
42 31 0.24
43 20 0.16
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (41 bp):
TAAGGTGGTTGCTAAGTGCTGATTCCCCGTATCCTTGATTA
Found at i:35242630 original size:31 final size:31
Alignment explanation
Indices: 35242590--35242650 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
35242580 ATTGACTTAG
*
35242590 TAATTTCTTAAGGCGAAATACTAGGAAGCAA
1 TAATGTCTTAAGGCGAAATACTAGGAAGCAA
35242621 TAATGTCTTAAGGCGAAATACTAGGAAGCA
1 TAATGTCTTAAGGCGAAATACTAGGAAGCA
35242651 TGGAATTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (31 bp):
TAATGTCTTAAGGCGAAATACTAGGAAGCAA
Found at i:35242963 original size:29 final size:30
Alignment explanation
Indices: 35242915--35242976 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
35242905 TATGATCAAA
*
35242915 AAAAGAAAAGAAAAAAGAGCATATGTATTC
1 AAAAGAAAAGAAAAAAGAGCATATGTACTC
* * *
35242945 AAAA-AAAAGTAAAAGGAGCATGTGTACTC
1 AAAAGAAAAGAAAAAAGAGCATATGTACTC
35242974 AAA
1 AAA
35242977 TACAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.58, C:0.08, G:0.18, T:0.16
Consensus pattern (30 bp):
AAAAGAAAAGAAAAAAGAGCATATGTACTC
Found at i:35252760 original size:2 final size:2
Alignment explanation
Indices: 35252753--35252786 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
35252743 ATTCAATTGA
35252753 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35252787 CGATGACTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35254555 original size:15 final size:15
Alignment explanation
Indices: 35254537--35254566 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35254527 ATTTTCATTT
35254537 TTAAAATTTAATTAC
1 TTAAAATTTAATTAC
*
35254552 TTAAAATTTGATTAC
1 TTAAAATTTAATTAC
35254567 AAATGTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (15 bp):
TTAAAATTTAATTAC
Found at i:35255415 original size:13 final size:13
Alignment explanation
Indices: 35255397--35255426 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35255387 AATAATCATA
35255397 AAAACTTTTAATG
1 AAAACTTTTAATG
*
35255410 AAAACTTTTAATT
1 AAAACTTTTAATG
35255423 AAAA
1 AAAA
35255427 GTAAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (13 bp):
AAAACTTTTAATG
Found at i:35256257 original size:15 final size:15
Alignment explanation
Indices: 35256237--35256283 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
35256227 CTAAGGGTTT
35256237 GCACATACAGAGTTC
1 GCACATACAGAGTTC
*
35256252 GCACAT--AGGGTTC
1 GCACATACAGAGTTC
* *
35256265 ACGCATACAGAGTTC
1 GCACATACAGAGTTC
35256280 GCAC
1 GCAC
35256284 CTAGGGGTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
13 10 0.42
15 14 0.58
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (15 bp):
GCACATACAGAGTTC
Found at i:35256263 original size:57 final size:57
Alignment explanation
Indices: 35256202--35256377 Score: 183
Period size: 57 Copynumber: 3.1 Consensus size: 57
35256192 GCAAACTTAG
* * * *
35256202 GGGTTCACGTAAGTAGGGCTCGCACCTAAGGGTTTGCACATACAGAGTTCGCACATA
1 GGGTTCACGCAAGTAGGGTTCGCACCTAGGGGTTTGCACATACAGAGTTCGCACCTA
* * * *
35256259 GGGTTCACGCATA-CAGAGTTCGCACCTAGGGGTTTGCACATCCAAAGTTCGCACCTA
1 GGGTTCACGCA-AGTAGGGTTCGCACCTAGGGGTTTGCACATACAGAGTTCGCACCTA
* * * * * * * * *
35256316 GTGCTCGCACAAGTAGGGTTTGCATCTAGGGGTTCGCACATATAGAGTTGGCACCTA
1 GGGTTCACGCAAGTAGGGTTCGCACCTAGGGGTTTGCACATACAGAGTTCGCACCTA
35256373 GGGTT
1 GGGTT
35256378 TGCACATATA
Statistics
Matches: 94, Mismatches: 23, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
56 1 0.01
57 92 0.98
58 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (57 bp):
GGGTTCACGCAAGTAGGGTTCGCACCTAGGGGTTTGCACATACAGAGTTCGCACCTA
Found at i:35256384 original size:28 final size:28
Alignment explanation
Indices: 35256221--35256393 Score: 150
Period size: 28 Copynumber: 6.1 Consensus size: 28
35256211 TAAGTAGGGC
*
35256221 TCGCACCTAAGGGTTTGCACATACAGAGT
1 TCGCACCT-AGGGTTCGCACATACAGAGT
* * *
35256250 TCGCACATAGGGTTCACGCATACAGAGT
1 TCGCACCTAGGGTTCGCACATACAGAGT
* * *
35256278 TCGCACCTAGGGGTTTGCACATCCAAAGT
1 TCGCACCTA-GGGTTCGCACATACAGAGT
* * * *
35256307 TCGCACCTAGTGCTCGCACA-AGTAGGGT
1 TCGCACCTAGGGTTCGCACATA-CAGAGT
* * *
35256335 TTGCATCTAGGGGTTCGCACATATAGAGT
1 TCGCACCTA-GGGTTCGCACATACAGAGT
* * *
35256364 TGGCACCTAGGGTTTGCACATATAGAGT
1 TCGCACCTAGGGTTCGCACATACAGAGT
35256392 TC
1 TC
35256394 ACATAGATAA
Statistics
Matches: 114, Mismatches: 26, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
28 62 0.54
29 51 0.45
30 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (28 bp):
TCGCACCTAGGGTTCGCACATACAGAGT
Found at i:35256803 original size:18 final size:18
Alignment explanation
Indices: 35256777--35256844 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 18
35256767 GTTCGCGATA
*
35256777 CAAGAGAGTTCGCACATG
1 CAAGGGAGTTCGCACATG
* *
35256795 CAAGGGAGTTTGCA-ATA
1 CAAGGGAGTTCGCACATG
* *
35256812 CAGGGGAGGGTT-GCTCATG
1 CAAGGGA--GTTCGCACATG
35256831 CAAGGGAGTTCGCA
1 CAAGGGAGTTCGCA
35256845 TAGCAGGGGG
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
17 11 0.29
18 16 0.42
19 11 0.29
ACGTcount: A:0.28, C:0.18, G:0.35, T:0.19
Consensus pattern (18 bp):
CAAGGGAGTTCGCACATG
Found at i:35258012 original size:26 final size:26
Alignment explanation
Indices: 35257982--35258032 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
35257972 TTCAAATTCA
*
35257982 TTTATGACATGTTT-TTTTTTAATAAT
1 TTTAT-ACATGTTTAATTTTTAATAAT
*
35258008 TTTATATATGTTTAATTTTTAATAA
1 TTTATACATGTTTAATTTTTAATAA
35258033 AAAATTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (26 bp):
TTTATACATGTTTAATTTTTAATAAT
Found at i:35258390 original size:12 final size:11
Alignment explanation
Indices: 35258372--35258422 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
35258362 TTAGAAGATA
35258372 AAAAAAATTAT
1 AAAAAAATTAT
* *
35258383 CCAAAAAAGTAT
1 -AAAAAAATTAT
35258395 AAAAAAATT-T
1 AAAAAAATTAT
* *
35258405 AAAAAAATAAG
1 AAAAAAATTAT
35258416 AAAAAAA
1 AAAAAAA
35258423 AACCTAGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
10 9 0.28
11 14 0.44
12 9 0.28
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (11 bp):
AAAAAAATTAT
Found at i:35263166 original size:16 final size:16
Alignment explanation
Indices: 35263130--35263173 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
35263120 ATTTTTCGGC
*
35263130 CATTTTAGGTTTAGGT
1 CATTTTAGATTTAGGT
* *
35263146 TATTTTAGATTTGGGT
1 CATTTTAGATTTAGGT
35263162 CA-TTTAGATTTA
1 CATTTTAGATTTA
35263174 ATAGTTAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.23, C:0.05, G:0.20, T:0.52
Consensus pattern (16 bp):
CATTTTAGATTTAGGT
Found at i:35263257 original size:16 final size:16
Alignment explanation
Indices: 35263236--35263272 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
35263226 TGTTTTAGTT
35263236 ATTTCGAGCTTGAATA
1 ATTTCGAGCTTGAATA
* *
35263252 ATTTCGTGCTTGGATA
1 ATTTCGAGCTTGAATA
35263268 ATTTC
1 ATTTC
35263273 CGGTTTCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (16 bp):
ATTTCGAGCTTGAATA
Found at i:35266501 original size:16 final size:18
Alignment explanation
Indices: 35266475--35266507 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35266465 ATAAAAATTA
35266475 TAAATTAATTTT-TCAAT
1 TAAATTAATTTTCTCAAT
35266492 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
35266508 CCCGATTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:35269127 original size:23 final size:23
Alignment explanation
Indices: 35269097--35269146 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
35269087 GGTTTCAATT
*
35269097 GAACAACCTTTTTCGCTACCCTC
1 GAACAACCTTCTTCGCTACCCTC
35269120 GAACAACCTTCTTCGCTACCCTC
1 GAACAACCTTCTTCGCTACCCTC
35269143 GAAC
1 GAAC
35269147 CACAAATTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.40, G:0.10, T:0.26
Consensus pattern (23 bp):
GAACAACCTTCTTCGCTACCCTC
Found at i:35269634 original size:12 final size:13
Alignment explanation
Indices: 35269593--35269634 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
35269583 TTTAATCAAC
*
35269593 TAATTTAATTAAT
1 TAATTTACTTAAT
*
35269606 TATATTTACTAAAT
1 TA-ATTTACTTAAT
35269620 TAATTT-CTTAAT
1 TAATTTACTTAAT
35269632 TAA
1 TAA
35269635 ATAATTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 8 0.32
13 6 0.24
14 11 0.44
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATTTACTTAAT
Found at i:35271471 original size:39 final size:39
Alignment explanation
Indices: 35271428--35271517 Score: 137
Period size: 39 Copynumber: 2.3 Consensus size: 39
35271418 TATAATAGAT
*
35271428 TATAACAAGATCTAGA-ATTTGTTGTAGATCCTCAAGTAA
1 TATAACAAGATCT-GACATTTGTTGCAGATCCTCAAGTAA
* *
35271467 TATAACGAGATCTGACATTTGTTGCAGATCCTCAGGTAA
1 TATAACAAGATCTGACATTTGTTGCAGATCCTCAAGTAA
35271506 TATAACAAGATC
1 TATAACAAGATC
35271518 CATCATTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 2 0.04
39 44 0.96
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (39 bp):
TATAACAAGATCTGACATTTGTTGCAGATCCTCAAGTAA
Found at i:35272045 original size:16 final size:15
Alignment explanation
Indices: 35272032--35272060 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35272022 AATTAATTAA
35272032 AAATT-TGTTTAATT
1 AAATTATGTTTAATT
35272046 AAATTATGTTTAATT
1 AAATTATGTTTAATT
35272061 GTTTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
AAATTATGTTTAATT
Found at i:35279502 original size:27 final size:27
Alignment explanation
Indices: 35279471--35279650 Score: 211
Period size: 27 Copynumber: 6.7 Consensus size: 27
35279461 CCTAAAATTT
* * *
35279471 GTAAAATGATCATAATGCCCCTATAGG
1 GTAAAATGACCGTAATGCCCTTATAGG
* *
35279498 GTAAAATGACTGTAATGCCCTTATAAG
1 GTAAAATGACCGTAATGCCCTTATAGG
* *
35279525 GTAAAATGACCGTAATGCCCTTGTAGC
1 GTAAAATGACCGTAATGCCCTTATAGG
* *
35279552 GTAAAATGACCGTAATGCCCATGTAGG
1 GTAAAATGACCGTAATGCCCTTATAGG
* *
35279579 GTAAAATGATCGTAATG-CCTCTGTAGG
1 GTAAAATGACCGTAATGCCCT-TATAGG
*
35279606 GTAAAATGACCTTAATGCCCTTATA-G
1 GTAAAATGACCGTAATGCCCTTATAGG
**
35279632 GTAAAATGACTATAATGCC
1 GTAAAATGACCGTAATGCC
35279651 TCTGTTAGGT
Statistics
Matches: 133, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
26 20 0.15
27 110 0.83
28 3 0.02
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (27 bp):
GTAAAATGACCGTAATGCCCTTATAGG
Found at i:35279609 original size:81 final size:80
Alignment explanation
Indices: 35279471--35279650 Score: 238
Period size: 81 Copynumber: 2.2 Consensus size: 80
35279461 CCTAAAATTT
* *
35279471 GTAAAATGATCATAATGCCCCTATAGGGTAAAATGACTGTAATGCCCTTATAAGGTAAAATGACC
1 GTAAAATGACCATAATGCCCATATAGGGTAAAATGACTGTAATGCCCTTATAAGGTAAAATGACC
*
35279536 GTAATGCCCTTGTAG
66 GTAATGCCCTTATAG
* * * *
35279551 CGTAAAATGACCGTAATGCCCATGTAGGGTAAAATGA-TCGTAATG-CCTCTGTAGGGTAAAATG
1 -GTAAAATGACCATAATGCCCATATAGGGTAAAATGACT-GTAATGCCCT-TATAAGGTAAAATG
*
35279614 ACCTTAATGCCCTTATAG
63 ACCGTAATGCCCTTATAG
*
35279632 GTAAAATGACTATAATGCC
1 GTAAAATGACCATAATGCC
35279651 TCTGTTAGGT
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
80 21 0.24
81 66 0.76
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (80 bp):
GTAAAATGACCATAATGCCCATATAGGGTAAAATGACTGTAATGCCCTTATAAGGTAAAATGACC
GTAATGCCCTTATAG
Found at i:35279687 original size:80 final size:81
Alignment explanation
Indices: 35279471--35279695 Score: 212
Period size: 81 Copynumber: 2.8 Consensus size: 81
35279461 CCTAAAATTT
* * * * *
35279471 GTAAAATGATCATAATGCCCCTATAGGGTAAAATGA-CTGTAATGCC-CTTATAA-GGTAAAATG
1 GTAAAATGACCATAATGCCCATGTAGGGTAAAATGATC-GTAATACCTC-CA-AAGGGTAAAATG
*
35279533 ACCGTAATGCCCTTGTAGC
63 ACCGTAATGCCCTTATAGC
* * ***
35279552 GTAAAATGACCGTAATGCCCATGTAGGGTAAAATGATCGTAATGCCTCTGTAGGGTAAAATGACC
1 GTAAAATGACCATAATGCCCATGTAGGGTAAAATGATCGTAATACCTCCAAAGGGTAAAATGACC
*
35279617 TTAATGCCCTTATAG-
66 GTAATGCCCTTATAGC
* * *
35279632 GTAAAATGACTATAATGCCTC-TGTTA-GGTGAATTGATCG-ATATACCTCCAAAGGGTAAAATG
1 GTAAAATGACCATAATGCC-CATG-TAGGGTAAAATGATCGTA-ATACCTCCAAAGGGTAAAATG
35279694 AC
63 AC
35279696 TATTTTTCCC
Statistics
Matches: 122, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
79 1 0.01
80 50 0.41
81 69 0.57
82 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (81 bp):
GTAAAATGACCATAATGCCCATGTAGGGTAAAATGATCGTAATACCTCCAAAGGGTAAAATGACC
GTAATGCCCTTATAGC
Found at i:35279800 original size:24 final size:23
Alignment explanation
Indices: 35279720--35279798 Score: 95
Period size: 24 Copynumber: 3.3 Consensus size: 23
35279710 AGGTTAAATG
* *
35279720 ACTGATTTGTCTATGATTTAAATA
1 ACTGATTTGTCTGTGATTT-TATA
*
35279744 ACTGATTTGTCTGTGATTGGTATA
1 ACTGATTTGTCTGTGATT-TTATA
* *
35279768 ACTGATTTGTTTGTGATTTTATG
1 ACTGATTTGTCTGTGATTTTATA
35279791 ACTGATTT
1 ACTGATTT
35279799 TGAGCATGGC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
23 11 0.23
24 37 0.77
ACGTcount: A:0.24, C:0.08, G:0.19, T:0.49
Consensus pattern (23 bp):
ACTGATTTGTCTGTGATTTTATA
Found at i:35279931 original size:27 final size:26
Alignment explanation
Indices: 35279861--35279960 Score: 103
Period size: 27 Copynumber: 3.8 Consensus size: 26
35279851 ATGGAGGAAG
* *
35279861 TACTG-TACTGGCGGCTCTGCCACAA
1 TACTGTTACTGGCAGCTTTGCCACAA
**
35279886 TTACTGTTACTGGTGGCTTTGCCACATA
1 -TACTGTTACTGGCAGCTTTGCCACA-A
** *
35279914 TACTGTTACTGGCAGCTTTGCTGCGA
1 TACTGTTACTGGCAGCTTTGCCACAA
*
35279940 TACTGTTGCTGGCAGCTTTGC
1 TACTGTTACTGGCAGCTTTGC
35279961 TGCGATGCTA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
26 26 0.41
27 37 0.58
28 1 0.02
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.34
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGCCACAA
Found at i:35279951 original size:26 final size:26
Alignment explanation
Indices: 35279913--35279966 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
35279903 TTTGCCACAT
35279913 ATACTGTTACTGGCAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCG
*
35279939 ATACTGTTGCTGGCAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCG
35279965 AT
1 AT
35279967 GCTATTGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.15, C:0.22, G:0.28, T:0.35
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGCTGCG
Found at i:35279978 original size:26 final size:26
Alignment explanation
Indices: 35279923--35279978 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
35279913 ATACTGTTAC
* *
35279923 TGGCAGCTTTGCTGCGATACTGTTGC
1 TGGCAGCTTTGCTGCGATACTATTGA
*
35279949 TGGCAGCTTTGCTGCGATGCTATTGA
1 TGGCAGCTTTGCTGCGATACTATTGA
35279975 TGGC
1 TGGC
35279979 TGTGTGCCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.12, C:0.21, G:0.32, T:0.34
Consensus pattern (26 bp):
TGGCAGCTTTGCTGCGATACTATTGA
Found at i:35280008 original size:32 final size:32
Alignment explanation
Indices: 35279966--35280042 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
35279956 TTTGCTGCGA
* *
35279966 TGCTATTGATGGCTGTGTGCCGATCATATCAC
1 TGCTACTGATGGCTGTGTGCCAATCATATCAC
* *
35279998 TGCTACTGATGGCTTTGTGCCAATCATATTAC
1 TGCTACTGATGGCTGTGTGCCAATCATATCAC
*
35280030 TG-TACTTATGGCT
1 TGCTACTGATGGCT
35280043 TATGACCATT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 10 0.25
32 30 0.75
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (32 bp):
TGCTACTGATGGCTGTGTGCCAATCATATCAC
Found at i:35280302 original size:28 final size:28
Alignment explanation
Indices: 35280270--35280328 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
35280260 TATATTACTG
35280270 ACATTGTTACTGTATTGGGCTAAGGCCC
1 ACATTGTTACTGTATTGGGCTAAGGCCC
**
35280298 ACATTGTTACTGTATTGGGCTTTGGCCC
1 ACATTGTTACTGTATTGGGCTAAGGCCC
35280326 ACA
1 ACA
35280329 CACTGGTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (28 bp):
ACATTGTTACTGTATTGGGCTAAGGCCC
Found at i:35280609 original size:15 final size:16
Alignment explanation
Indices: 35280584--35280616 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
35280574 TGATAAGGCC
*
35280584 TTTATAATTTTTGGAT
1 TTTATAATTTTGGGAT
35280600 TTTA-AATTTTGGGAT
1 TTTATAATTTTGGGAT
35280615 TT
1 TT
35280617 GATTTGATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (16 bp):
TTTATAATTTTGGGAT
Found at i:35280714 original size:24 final size:24
Alignment explanation
Indices: 35280687--35280735 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
35280677 TTTCTAACGT
35280687 ACGTTTCCGCAACTCAATTTTTAA
1 ACGTTTCCGCAACTCAATTTTTAA
35280711 ACGTTTCCGCAACTCAATTTTTAA
1 ACGTTTCCGCAACTCAATTTTTAA
35280735 A
1 A
35280736 TATCACATTT
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:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (24 bp):
ACGTTTCCGCAACTCAATTTTTAA
Found at i:35302240 original size:31 final size:31
Alignment explanation
Indices: 35302205--35302296 Score: 166
Period size: 31 Copynumber: 3.0 Consensus size: 31
35302195 AAACAAATAA
35302205 AAAAAGATGGGAGTAAACATAAGCAAATTCT
1 AAAAAGATGGGAGTAAACATAAGCAAATTCT
*
35302236 AAAAAGATGGGAGTAAACATAAGAAAATTCT
1 AAAAAGATGGGAGTAAACATAAGCAAATTCT
*
35302267 AAAAAGATGGGAGTAAACAGAAGCAAATTC
1 AAAAAGATGGGAGTAAACATAAGCAAATTC
35302297 ATCTTGCAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.17
Consensus pattern (31 bp):
AAAAAGATGGGAGTAAACATAAGCAAATTCT
Found at i:35309531 original size:29 final size:28
Alignment explanation
Indices: 35309484--35309540 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
35309474 CTCTTCAAGC
35309484 TTTGATTTTTATATTTTCATGAATTCAT
1 TTTGATTTTTATATTTTCATGAATTCAT
* *
35309512 TTTGATTTTTATCTATTTCATGCATTCAT
1 TTTGATTTTTATAT-TTTCATGAATTCAT
35309541 GTAGGTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.60
Consensus pattern (28 bp):
TTTGATTTTTATATTTTCATGAATTCAT
Found at i:35309549 original size:29 final size:28
Alignment explanation
Indices: 35309487--35309549 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
35309477 TTCAAGCTTT
* *
35309487 GATTTTTATATTTTCATGAATTCATTTT
1 GATTTTTATATTTTCATGAATTCATGTA
* *
35309515 GATTTTTATCTATTTCATGCATTCATGTA
1 GATTTTTATAT-TTTCATGAATTCATGTA
*
35309544 GGTTTT
1 GATTTT
35309550 ATTCATTTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 10 0.34
29 19 0.66
ACGTcount: A:0.22, C:0.10, G:0.11, T:0.57
Consensus pattern (28 bp):
GATTTTTATATTTTCATGAATTCATGTA
Found at i:35324396 original size:20 final size:20
Alignment explanation
Indices: 35324371--35324408 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35324361 ATCAAAACAT
35324371 TATAAA-GAAAACAAAACTAA
1 TATAAAGGAAAA-AAAACTAA
35324391 TATAAAGGAAAAAAAACT
1 TATAAAGGAAAAAAAACT
35324409 TGGTGAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (20 bp):
TATAAAGGAAAAAAAACTAA
Found at i:35341688 original size:13 final size:13
Alignment explanation
Indices: 35341670--35341699 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35341660 AAGAAAAAGG
35341670 CATTCATCTTCTA
1 CATTCATCTTCTA
*
35341683 CATTCATCTTCTT
1 CATTCATCTTCTA
35341696 CATT
1 CATT
35341700 TATGAAGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.30, G:0.00, T:0.50
Consensus pattern (13 bp):
CATTCATCTTCTA
Found at i:35343150 original size:27 final size:27
Alignment explanation
Indices: 35343112--35343171 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
35343102 TCAGTTGTTG
35343112 TTTTGGTTATAATGACATGTATAGGTA
1 TTTTGGTTATAATGACATGTATAGGTA
* *
35343139 TTTTGGTTATAATGGCATGTATTGGTA
1 TTTTGGTTATAATGACATGTATAGGTA
35343166 TTTTGG
1 TTTTGG
35343172 CTAATGTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.23, C:0.03, G:0.25, T:0.48
Consensus pattern (27 bp):
TTTTGGTTATAATGACATGTATAGGTA
Found at i:35345586 original size:31 final size:31
Alignment explanation
Indices: 35345548--35345610 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
35345538 TAGTACAGTA
35345548 TACAAGGTATGAAAATG-AAAATACGAATGAT
1 TACAAGGTATGAAAATGCAAAA-ACGAATGAT
* *
35345579 TACAAGGTATGAATATGCAAAAATGAATGAT
1 TACAAGGTATGAAAATGCAAAAACGAATGAT
35345610 T
1 T
35345611 GATGCCCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.25
Consensus pattern (31 bp):
TACAAGGTATGAAAATGCAAAAACGAATGAT
Found at i:35348946 original size:2 final size:2
Alignment explanation
Indices: 35348939--35348974 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
35348929 ATAAAAAGTG
35348939 GA GA GA GA GA GA GA GA G- GA GA GA GA GA G- GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
35348975 AAACAAGCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35348961 original size:11 final size:11
Alignment explanation
Indices: 35348939--35348974 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
35348929 ATAAAAAGTG
35348939 GAGAGA-GAGA
1 GAGAGAGGAGA
35348949 GAGAGAGGAGA
1 GAGAGAGGAGA
35348960 GAGAGAGGAGA
1 GAGAGAGGAGA
35348971 GAGA
1 GAGA
35348975 AAACAAGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (11 bp):
GAGAGAGGAGA
Found at i:35355625 original size:16 final size:17
Alignment explanation
Indices: 35355594--35355628 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
35355584 TATTTCAATC
*
35355594 CAAAATTCATACTTTTG
1 CAAAATTCAGACTTTTG
35355611 CAAAATT-AGACTTTTG
1 CAAAATTCAGACTTTTG
35355627 CA
1 CA
35355629 CTTAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (17 bp):
CAAAATTCAGACTTTTG
Found at i:35361999 original size:29 final size:29
Alignment explanation
Indices: 35361899--35362008 Score: 114
Period size: 29 Copynumber: 3.8 Consensus size: 29
35361889 GTGCTAAACA
* *
35361899 ATGGTCATAACCATCCCTTTTCAT-GTTTG
1 ATGGTCGTCACCATCCCTTTTCATAG-TTG
* ** * * *
35361928 ATGGTTGAAACCATCCCTTTTAATTAATCG
1 ATGGTCGTCACCATCCCTTTTCA-TAGTTG
35361958 ATGGTCGTCACCATCCCTTTTCATAGTTG
1 ATGGTCGTCACCATCCCTTTTCATAGTTG
*
35361987 GTGGTCGTCACCATCCCTTTTC
1 ATGGTCGTCACCATCCCTTTTC
35362009 TTAATCGATA
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
29 44 0.67
30 22 0.33
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.38
Consensus pattern (29 bp):
ATGGTCGTCACCATCCCTTTTCATAGTTG
Found at i:35362000 original size:59 final size:58
Alignment explanation
Indices: 35361899--35362039 Score: 160
Period size: 59 Copynumber: 2.4 Consensus size: 58
35361889 GTGCTAAACA
* *
35361899 ATGGTCATAACCATCCCTTTTCATGTTTGATGGTTGAAACCATCCCTTTTAATTAATCG
1 ATGGTCGTAACCATCCCTTTTCATGTTTGATGGTCGAAACCATCCCTTTT-ATTAATCG
* * ** *
35361958 ATGGTCGTCACCATCCCTTTTCATAG-TTGGTGGTCGTCACCATCCCTTTTCTTAATCG
1 ATGGTCGTAACCATCCCTTTTCAT-GTTTGATGGTCGAAACCATCCCTTTTATTAATCG
* *
35362016 ATAGTCG-AAGCTATCCCTTTTCAT
1 ATGGTCGTAA-CCATCCCTTTTCAT
35362040 TGGTCGATGA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
57 1 0.01
58 26 0.37
59 42 0.60
60 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (58 bp):
ATGGTCGTAACCATCCCTTTTCATGTTTGATGGTCGAAACCATCCCTTTTATTAATCG
Found at i:35362022 original size:29 final size:29
Alignment explanation
Indices: 35361937--35362022 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
35361927 GATGGTTGAA
*
35361937 ACCATCCCTTTTAATTAATCGATGGTCGTC
1 ACCATCCCTTTT-CTTAATCGATGGTCGTC
* * * *
35361967 ACCATCCCTTTTCATAGTTGGTGGTCGTC
1 ACCATCCCTTTTCTTAATCGATGGTCGTC
*
35361996 ACCATCCCTTTTCTTAATCGATAGTCG
1 ACCATCCCTTTTCTTAATCGATGGTCG
35362023 AAGCTATCCC
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
29 34 0.74
30 12 0.26
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.37
Consensus pattern (29 bp):
ACCATCCCTTTTCTTAATCGATGGTCGTC
Found at i:35372756 original size:16 final size:17
Alignment explanation
Indices: 35372735--35372775 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
35372725 ACTTGCAAAT
*
35372735 TTTTTTTTAATTTG-AA
1 TTTTTTTTAATTCGAAA
35372751 -TTTTTTTAATTCGAAA
1 TTTTTTTTAATTCGAAA
35372767 TTCTTTTTT
1 TT-TTTTTT
35372776 TAAATGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 1 0.05
18 6 0.29
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTTTTTTAATTCGAAA
Found at i:35372838 original size:12 final size:13
Alignment explanation
Indices: 35372820--35372856 Score: 53
Period size: 11 Copynumber: 3.1 Consensus size: 13
35372810 TTTTTACTCA
35372820 AACTTTTTTTTCG
1 AACTTTTTTTTCG
35372833 AA-TTTTTTTT--
1 AACTTTTTTTTCG
35372843 AACTTTTTTTTCG
1 AACTTTTTTTTCG
35372856 A
1 A
35372857 TACTACAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
10 2 0.10
11 8 0.38
12 8 0.38
13 3 0.14
ACGTcount: A:0.19, C:0.11, G:0.05, T:0.65
Consensus pattern (13 bp):
AACTTTTTTTTCG
Found at i:35373797 original size:14 final size:14
Alignment explanation
Indices: 35373778--35373806 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
35373768 ACTAGCTGCA
35373778 CATGCATGAATCTT
1 CATGCATGAATCTT
35373792 CATGCATGAATCTT
1 CATGCATGAATCTT
35373806 C
1 C
35373807 CCAATGAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (14 bp):
CATGCATGAATCTT
Found at i:35379329 original size:89 final size:89
Alignment explanation
Indices: 35379178--35379345 Score: 300
Period size: 89 Copynumber: 1.9 Consensus size: 89
35379168 GCATATCAAC
* *
35379178 CATATCAACTTATTTGAGCATGGCCATTCATTTCTAGTCTCACTCAATCAAGTGGCCTAAGATAT
1 CATATCAACTTATTTGAGCATGGCCATGCAATTCTAGTCTCACTCAATCAAGTGGCCTAAGATAT
*
35379243 TACTCCTATTATGTTCAATCATCT
66 TACTCCCATTATGTTCAATCATCT
*
35379267 CATATCAACTTATTTGAGCATGGCCATGCAATTCTAGTCTCACTCAATCAAGTGGCTTAAGATAT
1 CATATCAACTTATTTGAGCATGGCCATGCAATTCTAGTCTCACTCAATCAAGTGGCCTAAGATAT
35379332 TACTCCCATTATGT
66 TACTCCCATTATGT
35379346 AGGAGGGACT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
89 75 1.00
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (89 bp):
CATATCAACTTATTTGAGCATGGCCATGCAATTCTAGTCTCACTCAATCAAGTGGCCTAAGATAT
TACTCCCATTATGTTCAATCATCT
Found at i:35382438 original size:25 final size:24
Alignment explanation
Indices: 35382410--35382486 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 24
35382400 AATAAATCTA
35382410 ATTTTTTAATAGTTATCAGAATTTT
1 ATTTTTTAATAGTTATC-GAATTTT
* * *
35382435 ATTTTATAATAACTATATCTAA--TT
1 ATTTTTTAAT-AGT-TATCGAATTTT
35382459 -TTTTTT-ATAGTTATCGGAATTTT
1 ATTTTTTAATAGTTATC-GAATTTT
35382482 ATTTT
1 ATTTT
35382487 ATTATAACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
20 4 0.10
21 4 0.10
22 2 0.05
23 7 0.17
24 6 0.15
25 9 0.22
26 4 0.10
27 4 0.10
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.57
Consensus pattern (24 bp):
ATTTTTTAATAGTTATCGAATTTT
Found at i:35382479 original size:47 final size:46
Alignment explanation
Indices: 35382405--35382497 Score: 150
Period size: 47 Copynumber: 2.0 Consensus size: 46
35382395 CAACTAATAA
35382405 ATCTAATTTTTTAATAGTTATCAGAATTTTATTTTATAATAACTAT
1 ATCTAATTTTTTAATAGTTATCAGAATTTTATTTTATAATAACTAT
* * *
35382451 ATCTAATTTTTTTTATAGTTATCGGAATTTTATTTTATTATAACTAT
1 ATCTAA-TTTTTTAATAGTTATCAGAATTTTATTTTATAATAACTAT
35382498 CATATACTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
46 6 0.14
47 37 0.86
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.55
Consensus pattern (46 bp):
ATCTAATTTTTTAATAGTTATCAGAATTTTATTTTATAATAACTAT
Found at i:35386582 original size:23 final size:23
Alignment explanation
Indices: 35386552--35386607 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
35386542 CGATTTGTGC
35386552 CCGTGTAACTCAGGGTCACACAG
1 CCGTGTAACTCAGGGTCACACAG
*
35386575 CCGTGTAACTCAGGGTCACATAG
1 CCGTGTAACTCAGGGTCACACAG
35386598 CCGTGTAACT
1 CCGTGTAACT
35386608 TACTGTGGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.21
Consensus pattern (23 bp):
CCGTGTAACTCAGGGTCACACAG
Found at i:35386738 original size:89 final size:89
Alignment explanation
Indices: 35386597--35386781 Score: 271
Period size: 89 Copynumber: 2.1 Consensus size: 89
35386587 GGGTCACATA
* *
35386597 GCCGTGTAACTTACTGTGGCCGTGTGAACTAAAAATCACCCTAAACGATAGCACACATGACCATG
1 GCCGTGTAACTCACTATGGCCGTGTGAACTAAAAATCACCCTAAACGATAGCACACATGACCATG
* * *
35386662 TCAATCACCCGTGTGTGGCACACG
66 CCAATCACCCATGTGTGACACACG
* * * * *
35386686 GCCGTGTAACTCACTATGGCTGTGTGAACTAAAAATCACCCTGAATGGTAGCACACATGGCCATG
1 GCCGTGTAACTCACTATGGCCGTGTGAACTAAAAATCACCCTAAACGATAGCACACATGACCATG
35386751 CCAATCACCCATGTGTGACACACG
66 CCAATCACCCATGTGTGACACACG
*
35386775 ACCGTGT
1 GCCGTGT
35386782 GGTAGCCCGT
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 85 1.00
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (89 bp):
GCCGTGTAACTCACTATGGCCGTGTGAACTAAAAATCACCCTAAACGATAGCACACATGACCATG
CCAATCACCCATGTGTGACACACG
Found at i:35387017 original size:23 final size:23
Alignment explanation
Indices: 35386989--35387047 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
35386979 ACAAATACAA
35386989 TTCATACTAAAACTTTTAACCAT
1 TTCATACTAAAACTTTTAACCAT
*
35387012 TTCATACTAAAGCTTTTAACCAT
1 TTCATACTAAAACTTTTAACCAT
*
35387035 TTCATACCAAAAC
1 TTCATACTAAAAC
35387048 ACTCAACTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.36
Consensus pattern (23 bp):
TTCATACTAAAACTTTTAACCAT
Found at i:35390035 original size:43 final size:40
Alignment explanation
Indices: 35389947--35390176 Score: 214
Period size: 43 Copynumber: 5.5 Consensus size: 40
35389937 TTCGGTGGAT
*
35389947 TCAGCACTTAGCAACCACC-TTA-AATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACC-CCTTTACAA-TCAAT-ATACGGGGAA
*
35389988 TCAGCACATAGCAACCCCTTTCACAATCAAATATACGGTGGAA
1 TCAGCACTTAGCAACCCCTTT-ACAATC-AATATACGG-GGAA
* * *
35390031 TCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACC-CCTTTACAATCAAT-ATACGGGGAA
*
35390073 TCAGCA-TATAGCAACCCCTTTCACAATCACATATATGGTGGAA
1 TCAGCACT-TAGCAACCCCTTT-ACAATCA-ATATACGG-GGAA
* * ** *
35390116 TCAACACTTAGCAACCACCTTTAAAATCAATAATTTGAGGAA
1 TCAGCACTTAGCAACC-CCTTTACAATCAAT-ATACGGGGAA
35390158 TCAGCACTTAGCAACCCCT
1 TCAGCACTTAGCAACCCCT
35390177 CGGGGAATCT
Statistics
Matches: 160, Mismatches: 15, Indels: 28
0.79 0.07 0.14
Matches are distributed among these distances:
40 2 0.01
41 26 0.16
42 60 0.38
43 61 0.38
44 11 0.07
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (40 bp):
TCAGCACTTAGCAACCCCTTTACAATCAATATACGGGGAA
Found at i:35390084 original size:85 final size:85
Alignment explanation
Indices: 35389939--35390176 Score: 352
Period size: 85 Copynumber: 2.8 Consensus size: 85
35389929 ATCTGTTATT
*
35389939 CGGTGGATTCAGCACTTAGCAACCACC-TTAAATTCAGTGATACGGGGAATCAGCACATAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAAC
35390003 CCCTTTCACAATCAAATATA
66 CCCTTTCACAATCAAATATA
* *
35390023 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAGCATATAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAAC
*
35390088 CCCTTTCACAATCACATATA
66 CCCTTTCACAATCAAATATA
* * * * * ** * *
35390108 TGGTGGAATCAACACTTAGCAACCACCTTTAAAATCAATAATTTGAGGAATCAGCACTTAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAAC
35390173 CCCT
66 CCCT
35390177 CGGGGAATCT
Statistics
Matches: 138, Mismatches: 15, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
84 26 0.19
85 112 0.81
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (85 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAAC
CCCTTTCACAATCAAATATA
Found at i:35390167 original size:42 final size:42
Alignment explanation
Indices: 35389947--35390173 Score: 214
Period size: 42 Copynumber: 5.4 Consensus size: 42
35389937 TTCGGTGGAT
* * *
35389947 TCAGCACTTAGCAACCACC-TTAAATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACCACCTTTAAAATCAATAATACGGGGAA
* *
35389988 TCAGCACATAGCAACC-CCTTTCACAATCAA-ATATACGGTGGAA
1 TCAGCACTTAGCAACCACCTTT-AAAATCAATA-ATACGG-GGAA
* * * *
35390031 TCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACCACCTTTAAAATCAATAATACGGGGAA
* *
35390073 TCAGCA-TATAGCAACC-CCTTTCACAATCACAT-ATATGGTGGAA
1 TCAGCACT-TAGCAACCACCTTT-AAAATCA-ATAATACGG-GGAA
* ** *
35390116 TCAACACTTAGCAACCACCTTTAAAATCAATAATTTGAGGAA
1 TCAGCACTTAGCAACCACCTTTAAAATCAATAATACGGGGAA
35390158 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
35390174 CCTCGGGGAA
Statistics
Matches: 154, Mismatches: 19, Indels: 25
0.78 0.10 0.13
Matches are distributed among these distances:
40 2 0.01
41 23 0.15
42 60 0.39
43 58 0.38
44 11 0.07
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.24
Consensus pattern (42 bp):
TCAGCACTTAGCAACCACCTTTAAAATCAATAATACGGGGAA
Found at i:35392669 original size:13 final size:13
Alignment explanation
Indices: 35392651--35392697 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
35392641 ATATTTCTGT
35392651 AAATATTTAATAA
1 AAATATTTAATAA
35392664 AAATATTT-ATAA
1 AAATATTTAATAA
**
35392676 ACTTGATTTAATAA
1 AAAT-ATTTAATAA
35392690 AAATATTT
1 AAATATTT
35392698 CAGACCGAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 6 0.21
13 16 0.57
14 6 0.21
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (13 bp):
AAATATTTAATAA
Found at i:35393408 original size:24 final size:25
Alignment explanation
Indices: 35393360--35393410 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
35393350 CCTCCTTAAA
* *
35393360 TCCAAATATTCTCTCCTCAAATCTC
1 TCCAAATATTCCCTCATCAAATCTC
*
35393385 TCCAAATA-TCCCTCATCAATTCTC
1 TCCAAATATTCCCTCATCAAATCTC
35393409 TC
1 TC
35393411 TATGACAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.27, C:0.37, G:0.00, T:0.35
Consensus pattern (25 bp):
TCCAAATATTCCCTCATCAAATCTC
Found at i:35396709 original size:17 final size:18
Alignment explanation
Indices: 35396677--35396710 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35396667 ATAAACATAA
*
35396677 AAATAAACACCTAAAAAG
1 AAATAAACAACTAAAAAG
35396695 AAATAAA-AACTAAAAA
1 AAATAAACAACTAAAAA
35396711 AAAGAATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.74, C:0.12, G:0.03, T:0.12
Consensus pattern (18 bp):
AAATAAACAACTAAAAAG
Found at i:35414834 original size:23 final size:23
Alignment explanation
Indices: 35414804--35414850 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
35414794 CCTTAATTCC
35414804 ATTAGTTTTATTTAACTTAGTTT
1 ATTAGTTTTATTTAACTTAGTTT
35414827 ATTAGTTTTATTTAACTTAGTTT
1 ATTAGTTTTATTTAACTTAGTTT
35414850 A
1 A
35414851 CTTTAATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.60
Consensus pattern (23 bp):
ATTAGTTTTATTTAACTTAGTTT
Found at i:35422528 original size:40 final size:40
Alignment explanation
Indices: 35422483--35422560 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
35422473 TTAGCCAAGT
35422483 TTGTTTAAGGATGCTCATAAATTCTATTAGTCATGCGCCG
1 TTGTTTAAGGATGCTCATAAATTCTATTAGTCATGCGCCG
35422523 TTGTTTAAGGATGCTCATAAATTCTATTAGTCATGCGC
1 TTGTTTAAGGATGCTCATAAATTCTATTAGTCATGCGC
35422561 TATTGTCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (40 bp):
TTGTTTAAGGATGCTCATAAATTCTATTAGTCATGCGCCG
Found at i:35432001 original size:25 final size:24
Alignment explanation
Indices: 35431973--35432069 Score: 90
Period size: 25 Copynumber: 4.0 Consensus size: 24
35431963 ACGAGCTATG
*
35431973 AATCGGTATGCTC-TCACAAGCTGGA
1 AATCGGTAAGCTCAT-ACAAGCT-GA
** *
35431998 AATCGGTAAGCTCATATGAGCTAA
1 AATCGGTAAGCTCATACAAGCTGA
* *
35432022 GAATCAGTAAGATC-TCACAAGCTGA
1 -AATCGGTAAGCTCAT-ACAAGCTGA
35432047 AATCGGTAAGCTCATACAAGCTG
1 AATCGGTAAGCTCATACAAGCTG
35432070 TGGTGTATCT
Statistics
Matches: 57, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
24 21 0.37
25 35 0.61
26 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.23
Consensus pattern (24 bp):
AATCGGTAAGCTCATACAAGCTGA
Found at i:35432038 original size:50 final size:49
Alignment explanation
Indices: 35431957--35432068 Score: 161
Period size: 50 Copynumber: 2.3 Consensus size: 49
35431947 GTACATGTAT
* * * *
35431957 GCTCATACGAGCTATGAATCGGTATGCTCTCACAAGCTGGAAATCGGTAA
1 GCTCATACGAGCTAAGAATCAGTAAGATCTCACAAGCT-GAAATCGGTAA
*
35432007 GCTCATATGAGCTAAGAATCAGTAAGATCTCACAAGCTGAAATCGGTAA
1 GCTCATACGAGCTAAGAATCAGTAAGATCTCACAAGCTGAAATCGGTAA
*
35432056 GCTCATACAAGCT
1 GCTCATACGAGCT
35432069 GTGGTGTATC
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
49 22 0.40
50 33 0.60
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (49 bp):
GCTCATACGAGCTAAGAATCAGTAAGATCTCACAAGCTGAAATCGGTAA
Found at i:35436549 original size:17 final size:17
Alignment explanation
Indices: 35436527--35436559 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35436517 GTTAGTGAAC
*
35436527 ATTGTCATTGCATTTTT
1 ATTGTCATCGCATTTTT
35436544 ATTGTCATCGCATTTT
1 ATTGTCATCGCATTTT
35436560 CATGTTCGCG
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:0.18, C:0.15, G:0.12, T:0.55
Consensus pattern (17 bp):
ATTGTCATCGCATTTTT
Found at i:35443999 original size:91 final size:91
Alignment explanation
Indices: 35443844--35444023 Score: 351
Period size: 91 Copynumber: 2.0 Consensus size: 91
35443834 AATCTTATAA
35443844 GTGCCTACGAAGGTTGATTAATTGTTTGAATTGGCATTGAGAAATTTTCAAGTGATTTGTTAATT
1 GTGCCTACGAAGGTTGATTAATTGTTTGAATTGGCATTGAGAAATTTTCAAGTGATTTGTTAATT
*
35443909 TAGTACGTATGTATATGCAATAGTAT
66 TAGTAAGTATGTATATGCAATAGTAT
35443935 GTGCCTACGAAGGTTGATTAATTGTTTGAATTGGCATTGAGAAATTTTCAAGTGATTTGTTAATT
1 GTGCCTACGAAGGTTGATTAATTGTTTGAATTGGCATTGAGAAATTTTCAAGTGATTTGTTAATT
35444000 TAGTAAGTATGTATATGCAATAGT
66 TAGTAAGTATGTATATGCAATAGT
35444024 TAGCAAATTA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (91 bp):
GTGCCTACGAAGGTTGATTAATTGTTTGAATTGGCATTGAGAAATTTTCAAGTGATTTGTTAATT
TAGTAAGTATGTATATGCAATAGTAT
Found at i:35449014 original size:27 final size:27
Alignment explanation
Indices: 35448984--35449136 Score: 177
Period size: 27 Copynumber: 5.7 Consensus size: 27
35448974 AATAGGCCTC
*
35448984 TAAAATTACCAAAATACCCTCAATGGG
1 TAAAATTACCGAAATACCCTCAATGGG
** *
35449011 TAAAATTACTAAAATACCC-CGATGGG
1 TAAAATTACCGAAATACCCTCAATGGG
* *
35449037 TAAAATTATCGAAATACCCTCGATGGG
1 TAAAATTACCGAAATACCCTCAATGGG
* *
35449064 TAAAATTACCGAAATACCCCTGAA-AGG
1 TAAAATTACCGAAATA-CCCTCAATGGG
*
35449091 TAAAATGACCGAAATACCCTCGAA-GGG
1 TAAAATTACCGAAATACCCTC-AATGGG
*
35449118 TAAAGTTACCGAAATACCC
1 TAAAATTACCGAAATACCC
35449137 CTATATGGTA
Statistics
Matches: 109, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
26 26 0.24
27 78 0.72
28 5 0.05
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.21
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCTCAATGGG
Found at i:35449119 original size:54 final size:54
Alignment explanation
Indices: 35448984--35449138 Score: 206
Period size: 54 Copynumber: 2.9 Consensus size: 54
35448974 AATAGGCCTC
* ** **
35448984 TAAAATTACCAAAATACCCTC-AATGGGTAAAATTACTAAAATACCCC-GATGGG
1 TAAAATTACCGAAATACCCTCGAA-GGGTAAAATTACCGAAATACCCCTGAAAGG
* *
35449037 TAAAATTATCGAAATACCCTCGATGGGTAAAATTACCGAAATACCCCTGAAAGG
1 TAAAATTACCGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCCTGAAAGG
* *
35449091 TAAAATGACCGAAATACCCTCGAAGGGTAAAGTTACCGAAATACCCCT
1 TAAAATTACCGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCCT
35449139 ATATGGTAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
53 40 0.45
54 49 0.55
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.21
Consensus pattern (54 bp):
TAAAATTACCGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCCTGAAAGG
Found at i:35449374 original size:26 final size:26
Alignment explanation
Indices: 35449345--35449447 Score: 107
Period size: 26 Copynumber: 4.0 Consensus size: 26
35449335 TTGCCACAAA
*
35449345 TACTGTTATTGGTAGCTTTGCTACGT
1 TACTGTTATTGGCAGCTTTGCTACGT
* * * *
35449371 TACTGATATTGGCAGCTCTGCTGCAT
1 TACTGTTATTGGCAGCTTTGCTACGT
* *
35449397 TACTGTTATTGGCAGCTTTTCTCCGT
1 TACTGTTATTGGCAGCTTTGCTACGT
* * * *
35449423 TACTATTACTGGTAGCTTTACTACG
1 TACTGTTATTGGCAGCTTTGCTACG
35449448 ATATTGGTGT
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 62 1.00
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.42
Consensus pattern (26 bp):
TACTGTTATTGGCAGCTTTGCTACGT
Done.