Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 137 of 182
Found at i:42859922 original size:14 final size:15
Alignment explanation
Indices: 42859903--42859932 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
42859893 TGTTTAAAAC
42859903 TTAATTAA-CCTTAA
1 TTAATTAATCCTTAA
42859917 TTAATTAATCCTTAA
1 TTAATTAATCCTTAA
42859932 T
1 T
42859933 CACAATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAATTAATCCTTAA
Found at i:42864534 original size:17 final size:17
Alignment explanation
Indices: 42864508--42864584 Score: 90
Period size: 17 Copynumber: 4.6 Consensus size: 17
42864498 GAGTGATGGG
42864508 TGTT-ACATTAAAAGCA
1 TGTTAACATTAAAAGCA
*
42864524 TGCTAACATTAAAAGCA
1 TGTTAACATTAAAAGCA
42864541 TGTTAACATTTAACATAG--
1 TGTTAACA-TTAA-A-AGCA
42864559 TGTT-ACATTAAAAGCA
1 TGTTAACATTAAAAGCA
42864575 TGTTAACATT
1 TGTTAACATT
42864585 CCATAACATA
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
14 2 0.04
15 1 0.02
16 11 0.21
17 27 0.52
18 8 0.15
19 1 0.02
20 2 0.04
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.34
Consensus pattern (17 bp):
TGTTAACATTAAAAGCA
Found at i:42865296 original size:22 final size:22
Alignment explanation
Indices: 42865275--42865321 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
42865265 GATTGAAATG
*
42865275 GATGATTAT-TTTTATATGAAT
1 GATGATTATATTTTAAATGAAT
*
42865296 GATGTTTATATTTTAAATGATAT
1 GATGATTATATTTTAAATGA-AT
42865319 GAT
1 GAT
42865322 AAAATAAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 9 0.41
23 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (22 bp):
GATGATTATATTTTAAATGAAT
Found at i:42873413 original size:16 final size:17
Alignment explanation
Indices: 42873381--42873413 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42873371 TATCTTTTTT
*
42873381 TATTTTAAATTTATATA
1 TATTTAAAATTTATATA
42873398 TATTTAAAATTT-TATA
1 TATTTAAAATTTATATA
42873414 ATCTATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTAAAATTTATATA
Found at i:42874533 original size:13 final size:13
Alignment explanation
Indices: 42874515--42874539 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42874505 AAATAATTAC
42874515 TAATGTGATTTAT
1 TAATGTGATTTAT
42874528 TAATGTGATTTA
1 TAATGTGATTTA
42874540 CCCTTATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
TAATGTGATTTAT
Found at i:42874837 original size:3 final size:3
Alignment explanation
Indices: 42874825--42874872 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
42874815 AAGTTGTGTT
42874825 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42874872 A
1 A
42874873 ACTTATAAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:42881269 original size:54 final size:54
Alignment explanation
Indices: 42881187--42881295 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
42881177 TCTGTCACCT
42881187 TTATTAATGAAACTTAGCTCAAGATGAAAGCCATCTAATTCCCTCATTGATAGA
1 TTATTAATGAAACTTAGCTCAAGATGAAAGCCATCTAATTCCCTCATTGATAGA
42881241 TTATTAATGAAACTTAGCTCAAGATGAAAGCCATCTAATTCCCTCATTGATAGA
1 TTATTAATGAAACTTAGCTCAAGATGAAAGCCATCTAATTCCCTCATTGATAGA
42881295 T
1 T
42881296 CTGCTACTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (54 bp):
TTATTAATGAAACTTAGCTCAAGATGAAAGCCATCTAATTCCCTCATTGATAGA
Found at i:42884451 original size:34 final size:34
Alignment explanation
Indices: 42884413--42884533 Score: 172
Period size: 34 Copynumber: 3.6 Consensus size: 34
42884403 ACTCAGTTAA
* * *
42884413 CCATCCAACACACCAGATGCTC-AAATGAGCCAAT
1 CCATCCAACACACCAAATGCTCGTAA-GAGCTAAT
* *
42884447 CCATCCAACACAACAAATGCTCGTAAGAGCTAGT
1 CCATCCAACACACCAAATGCTCGTAAGAGCTAAT
*
42884481 CCATCCAACACACCAAATGCTCGTAAGAGCTATT
1 CCATCCAACACACCAAATGCTCGTAAGAGCTAAT
42884515 CCATCCAACACACCAAATG
1 CCATCCAACACACCAAATG
42884534 TATTGTAACA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
34 77 0.97
35 2 0.03
ACGTcount: A:0.38, C:0.34, G:0.12, T:0.17
Consensus pattern (34 bp):
CCATCCAACACACCAAATGCTCGTAAGAGCTAAT
Found at i:42886739 original size:2 final size:2
Alignment explanation
Indices: 42886732--42886764 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
42886722 CTATAAACTG
42886732 AT AT AT AT AT AT AT A- AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42886765 AGCTTTCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:42886752 original size:11 final size:11
Alignment explanation
Indices: 42886732--42886764 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
42886722 CTATAAACTG
42886732 ATAT-ATATAT
1 ATATAATATAT
42886742 ATATAATATAT
1 ATATAATATAT
42886753 ATATAATATAT
1 ATATAATATAT
42886764 A
1 A
42886765 AGCTTTCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
ATATAATATAT
Found at i:42894367 original size:12 final size:12
Alignment explanation
Indices: 42894350--42894381 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
42894340 AATTTTGATT
42894350 TTCTCCTTCATC
1 TTCTCCTTCATC
42894362 TTCTCCTTCATC
1 TTCTCCTTCATC
42894374 TTCATCCT
1 TTC-TCCT
42894382 CTTATTGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.09, C:0.41, G:0.00, T:0.50
Consensus pattern (12 bp):
TTCTCCTTCATC
Found at i:42899037 original size:23 final size:21
Alignment explanation
Indices: 42899007--42899052 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
42898997 AAGATATATT
42899007 AACACAAATAAGACGACAAAATA
1 AACACAAATAA-AC-ACAAAATA
*
42899030 AACACAAATAAACAGAAAATA
1 AACACAAATAAACACAAAATA
42899051 AA
1 AA
42899053 ATAATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.70, C:0.15, G:0.07, T:0.09
Consensus pattern (21 bp):
AACACAAATAAACACAAAATA
Found at i:42899405 original size:30 final size:29
Alignment explanation
Indices: 42899221--42899415 Score: 146
Period size: 29 Copynumber: 6.7 Consensus size: 29
42899211 ATTTAAAAAA
* * *
42899221 GGGTCAAAA-TGAAATTTTGGAGAGTTTG
1 GGGTCAAAACTTAATTTTTGGAAAGTTTG
** *
42899249 GGACCAAAA-TATAATTTTTGGAAAGTTCG
1 GGGTCAAAACT-TAATTTTTGGAAAGTTTG
* * *
42899278 GGGGC-AAATTTGAATTTTTAGAAAGTTTG
1 GGGTCAAAACTT-AATTTTTGGAAAGTTTG
* *
42899307 GGGTCAAATCTAAATTTTTGGAAAGTTTG
1 GGGTCAAAACTTAATTTTTGGAAAGTTTG
* * * * *
42899336 GGCATCCAATC-CAAATTTTGAGAAAGTTTG
1 GG-GTCAAAACTTAATTTTTG-GAAAGTTTG
42899366 AGGGTCAAAACTTAATTTTTGGAAAGTTTAG
1 -GGGTCAAAACTTAATTTTTGGAAAGTTT-G
* *
42899397 GGGTCAAAACATATTTTTT
1 GGGTCAAAACTTAATTTTT
42899416 TTTGGATAGT
Statistics
Matches: 132, Mismatches: 26, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
28 12 0.09
29 62 0.47
30 48 0.36
31 10 0.08
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (29 bp):
GGGTCAAAACTTAATTTTTGGAAAGTTTG
Found at i:42899448 original size:33 final size:33
Alignment explanation
Indices: 42899381--42899448 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
42899371 CAAAACTTAA
* *
42899381 TTTTTGGAAAGTTTAGGGGTCAAAACATATTTT
1 TTTTTGGAAAGTTTAGGGGTCAAAACACAATTT
*
42899414 TTTTTGGATAGTTTTA-GGGTCAAAACACAATTT
1 TTTTTGGAAAG-TTTAGGGGTCAAAACACAATTT
42899447 TT
1 TT
42899449 AAATGCAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 27 0.87
34 4 0.13
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.44
Consensus pattern (33 bp):
TTTTTGGAAAGTTTAGGGGTCAAAACACAATTT
Found at i:42900874 original size:30 final size:30
Alignment explanation
Indices: 42900704--42900912 Score: 153
Period size: 30 Copynumber: 7.0 Consensus size: 30
42900694 AAAAATAAAG
* * *
42900704 TTTGGAAAGTTTAAGGCT-AAAACATAATT
1 TTTGGAAAGTTTGAGGGTCAAAACTTAATT
** * *
42900733 TTTGGAAAGTTCAAGGGT-TAAATTTGAATT
1 TTTGGAAAGTTTGAGGGTCAAAACTT-AATT
* * * *
42900763 TTTGGGAAGTTTGGGGGTCAAATCTAAATT
1 TTTGGAAAGTTTGAGGGTCAAAACTTAATT
*
42900793 TTTAGG-AAGTTT-AGAGGT-AAAATCTAAATT
1 TTT-GGAAAGTTTGAG-GGTCAAAA-CTTAATT
*
42900823 TTTGGATAGTTTG-GGGTCAAAACTTAATT
1 TTTGGAAAGTTTGAGGGTCAAAACTTAATT
* * * *
42900852 TTTGAAAAGTTCGAGGGTCAAAACATACTT
1 TTTGGAAAGTTTGAGGGTCAAAACTTAATT
* *
42900882 TGTGGATAGTTTGAGGGTCAAAA-TATAATT
1 TTTGGAAAGTTTGAGGGTCAAAACT-TAATT
42900912 T
1 T
42900913 CTAAATAAAA
Statistics
Matches: 142, Mismatches: 28, Indels: 19
0.75 0.15 0.10
Matches are distributed among these distances:
29 45 0.32
30 92 0.65
31 5 0.04
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (30 bp):
TTTGGAAAGTTTGAGGGTCAAAACTTAATT
Found at i:42901075 original size:23 final size:23
Alignment explanation
Indices: 42901031--42901079 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
42901021 GGGTGAATTT
* *
42901031 AAAATAAATTAAAATAGCACAAA
1 AAAATAAATTAAAACAGAACAAA
42901054 AAAACTAAATTAAAACA-AACAAA
1 AAAA-TAAATTAAAACAGAACAAA
42901077 AAA
1 AAA
42901080 TGAGAAAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.73, C:0.10, G:0.02, T:0.14
Consensus pattern (23 bp):
AAAATAAATTAAAACAGAACAAA
Found at i:42901974 original size:23 final size:23
Alignment explanation
Indices: 42901948--42902006 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
42901938 TAAAATATAA
*
42901948 AATATTTTATATTAATTTA-ATTT
1 AATATTTTATATTAAATTATA-TT
*
42901971 AATATTTTATAATAAATTATATT
1 AATATTTTATATTAAATTATATT
*
42901994 AAAATTTTATATT
1 AATATTTTATATT
42902007 TTTATATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 30 0.97
24 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AATATTTTATATTAAATTATATT
Found at i:42902018 original size:31 final size:30
Alignment explanation
Indices: 42901966--42902029 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
42901956 ATATTAATTT
*
42901966 AATTTAATATTTTATAATAAATTATATTAA
1 AATTTAATATTTTATAATAAATTATACTAA
* *
42901996 AATTTTATATTTTTATATTAAATTATACTAA
1 AATTTAATA-TTTTATAATAAATTATACTAA
42902027 AAT
1 AAT
42902030 ATTTTAGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
AATTTAATATTTTATAATAAATTATACTAA
Found at i:42907945 original size:18 final size:17
Alignment explanation
Indices: 42907922--42907956 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
42907912 GAAATATTTG
42907922 ATTATAATATATTTTTTA
1 ATTAT-ATATATTTTTTA
*
42907940 ATTATATATTTTTTTTA
1 ATTATATATATTTTTTA
42907957 TAAAATAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTATATATATTTTTTA
Found at i:42911229 original size:32 final size:32
Alignment explanation
Indices: 42911188--42911501 Score: 247
Period size: 32 Copynumber: 9.8 Consensus size: 32
42911178 CATGAAATAA
* * *
42911188 TGTTCATAGATTAATAGCTAC-TACGATCTTAT
1 TGTTCATAGATTGACAGCT-CTTACGAGCTTAT
*
42911220 TGTTCATAGATTGACAGCTCTTACGAGCTTCT
1 TGTTCATAGATTGACAGCTCTTACGAGCTTAT
* * *
42911252 TATTCATAGATTGACAACTCTTATGAGCTTAT
1 TGTTCATAGATTGACAGCTCTTACGAGCTTAT
* *
42911284 TGTTCAAAGATTGACAGGTCTTACGAGCTTAT
1 TGTTCATAGATTGACAGCTCTTACGAGCTTAT
* * * *
42911316 TGATCATAGATTGATAGCTCTTATGAGCTTAC
1 TGTTCATAGATTGACAGCTCTTACGAGCTTAT
* * * * *
42911348 TGTTCACAGATTGATAACTCTTATGAG-TATAC
1 TGTTCATAGATTGACAGCTCTTACGAGCT-TAT
* * * *
42911380 TATTCACAGATTGATAGCTCCTACGAGCTTAT
1 TGTTCATAGATTGACAGCTCTTACGAGCTTAT
* * * * * *
42911412 TATTTATAGATTGATAGCTCTTATGAG-TACAC
1 TGTTCATAGATTGACAGCTCTTACGAGCT-TAT
* * * * *
42911444 TGTTCACAAATTGATAGCTCTTATGAGCATAT
1 TGTTCATAGATTGACAGCTCTTACGAGCTTAT
* * * *
42911476 TGTTAATAGATTAATAGCTCATACGA
1 TGTTCATAGATTGACAGCTCTTACGA
42911502 ATATATTGGA
Statistics
Matches: 231, Mismatches: 46, Indels: 10
0.80 0.16 0.03
Matches are distributed among these distances:
31 3 0.01
32 227 0.98
33 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (32 bp):
TGTTCATAGATTGACAGCTCTTACGAGCTTAT
Found at i:42911295 original size:64 final size:64
Alignment explanation
Indices: 42911190--42911501 Score: 274
Period size: 64 Copynumber: 4.9 Consensus size: 64
42911180 TGAAATAATG
* * *
42911190 TTCATAGATTAATAGCTAC-TACGATCTTATTGTTCATAGATTGACAGCTCTTACGAGCTTCTTA
1 TTCATAGATTGATAGCT-CTTATGAGCTTATTGTTCATAGATTGACAGCTCTTACGAGCTTCTTA
* * * * *
42911254 TTCATAGATTGACAACTCTTATGAGCTTATTGTTCAAAGATTGACAGGTCTTACGAGCTTATTGA
1 TTCATAGATTGATAGCTCTTATGAGCTTATTGTTCATAGATTGACAGCTCTTACGAGCTTCTT-A
* * * * *
42911319 -TCATAGATTGATAGCTCTTATGAGCTTACTGTTCACAGATTGATAACTCTTATGAG-TATAC-T
1 TTCATAGATTGATAGCTCTTATGAGCTTATTGTTCATAGATTGACAGCTCTTACGAGCT-T-CTT
42911381 A
64 A
* * * * * * * * * *
42911382 TTCACAGATTGATAGCTCCTACGAGCTTATTATTTATAGATTGATAGCTCTTATGAG-TACACTG
1 TTCATAGATTGATAGCTCTTATGAGCTTATTGTTCATAGATTGACAGCTCTTACGAGCTTC-TTA
* * * * * * *
42911446 TTCACAAATTGATAGCTCTTATGAGCATATTGTTAATAGATTAATAGCTCATACGA
1 TTCATAGATTGATAGCTCTTATGAGCTTATTGTTCATAGATTGACAGCTCTTACGA
42911502 ATATATTGGA
Statistics
Matches: 205, Mismatches: 36, Indels: 14
0.80 0.14 0.05
Matches are distributed among these distances:
62 1 0.00
63 3 0.01
64 200 0.98
65 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (64 bp):
TTCATAGATTGATAGCTCTTATGAGCTTATTGTTCATAGATTGACAGCTCTTACGAGCTTCTTA
Found at i:42911487 original size:96 final size:96
Alignment explanation
Indices: 42911188--42911501 Score: 330
Period size: 96 Copynumber: 3.3 Consensus size: 96
42911178 CATGAAATAA
* * * * * * *
42911188 TGTTCATAGATTAATAGCTACTACGATCTTATTGTTCATAGATTGACAGCTCTTACGAGCTTC-T
1 TGTTAATAGATTAATAGCTCCTACGAGCTTATTATTCATAGATTGATAGCTCTTATGAGC-TCAC
* * * *
42911252 TATTCATAGATTGACAACTCTTATGAGCTTAT
65 TGTTCACAGATTGATAACTCTTATGAGCATAT
* * * * *
42911284 TGTTCAA-AGATTGACAGGTCTTACGAGCTTATTGA-TCATAGATTGATAGCTCTTATGAGCTTA
1 TGTT-AATAGATTAATAGCTCCTACGAGCTTATT-ATTCATAGATTGATAGCTCTTATGAGCTCA
* *
42911347 CTGTTCACAGATTGATAACTCTTATGAGTATAC
64 CTGTTCACAGATTGATAACTCTTATGAGCATAT
* * * * *
42911380 TATTCACAGATTGATAGCTCCTACGAGCTTATTATTTATAGATTGATAGCTCTTATGAG-TACAC
1 TGTTAATAGATTAATAGCTCCTACGAGCTTATTATTCATAGATTGATAGCTCTTATGAGCT-CAC
* *
42911444 TGTTCACAAATTGATAGCTCTTATGAGCATAT
65 TGTTCACAGATTGATAACTCTTATGAGCATAT
*
42911476 TGTTAATAGATTAATAGCTCATACGA
1 TGTTAATAGATTAATAGCTCCTACGA
42911502 ATATATTGGA
Statistics
Matches: 178, Mismatches: 34, Indels: 12
0.79 0.15 0.05
Matches are distributed among these distances:
95 4 0.02
96 173 0.97
97 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (96 bp):
TGTTAATAGATTAATAGCTCCTACGAGCTTATTATTCATAGATTGATAGCTCTTATGAGCTCACT
GTTCACAGATTGATAACTCTTATGAGCATAT
Found at i:42912309 original size:19 final size:20
Alignment explanation
Indices: 42912285--42912322 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42912275 CCCTGTAAGG
42912285 TAAAAT-TTTTAGTTTTGTC
1 TAAAATGTTTTAGTTTTGTC
*
42912304 TAAAATGTTTTTGTTTTGT
1 TAAAATGTTTTAGTTTTGT
42912323 TCAGGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.03, G:0.13, T:0.61
Consensus pattern (20 bp):
TAAAATGTTTTAGTTTTGTC
Found at i:42916948 original size:13 final size:13
Alignment explanation
Indices: 42916932--42917031 Score: 53
Period size: 13 Copynumber: 7.5 Consensus size: 13
42916922 GTTTTTCAAA
* *
42916932 AAAGTTAACGGTC
1 AAAGTCAACAGTC
42916945 AAAGTCAACAGTC
1 AAAGTCAACAGTC
*
42916958 AACGATCAA-AGGTC
1 AAAG-TCAACA-GTC
*
42916972 AACTGTCAA-AGTC
1 AA-AGTCAACAGTC
* *
42916985 AACGGTCAACGGTC
1 AA-AGTCAACAGTC
*
42916999 AAAGGT-AACGGTC
1 AAA-GTCAACAGTC
*
42917012 AAAGTCAACGGTC
1 AAAGTCAACAGTC
42917025 AACAGTC
1 AA-AGTC
42917032 GGTCAACGAT
Statistics
Matches: 73, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
12 2 0.03
13 45 0.62
14 25 0.34
15 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (13 bp):
AAAGTCAACAGTC
Found at i:42916959 original size:7 final size:7
Alignment explanation
Indices: 42916942--42917031 Score: 59
Period size: 7 Copynumber: 13.4 Consensus size: 7
42916932 AAAGTTAACG
42916942 GTCAA-A
1 GTCAACA
42916948 GTCAACA
1 GTCAACA
42916955 GTCAAC-
1 GTCAACA
42916961 GATCAA-A
1 G-TCAACA
*
42916968 GGTCAACT
1 -GTCAACA
42916976 GTCAA-A
1 GTCAACA
*
42916982 GTCAACG
1 GTCAACA
*
42916989 GTCAACG
1 GTCAACA
42916996 GTCAA-A
1 GTCAACA
*
42917002 GGT-AACG
1 -GTCAACA
42917009 GTCAA-A
1 GTCAACA
*
42917015 GTCAACG
1 GTCAACA
42917022 GTCAACA
1 GTCAACA
42917029 GTC
1 GTC
42917032 GGTCAACGAT
Statistics
Matches: 66, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
6 20 0.30
7 45 0.68
8 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (7 bp):
GTCAACA
Found at i:42916972 original size:14 final size:13
Alignment explanation
Indices: 42916941--42917027 Score: 54
Period size: 13 Copynumber: 6.5 Consensus size: 13
42916931 AAAAGTTAAC
*
42916941 GGTCAAAGTCAACA
1 GGTCAACGTCAA-A
42916955 -GTCAACGATCAAA
1 GGTCAACG-TCAAA
42916968 GGTCAACTGTCAAA
1 GGTCAAC-GTCAAA
*
42916982 -GTCAACGGTCAAC
1 GGTCAAC-GTCAAA
* *
42916995 GGTCAAAGGT-AAC
1 GGTC-AACGTCAAA
* *
42917008 GGTCAAAGTCAAC
1 GGTCAACGTCAAA
42917021 GGTCAAC
1 GGTCAAC
42917028 AGTCGGTCAA
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
12 4 0.07
13 34 0.56
14 20 0.33
15 3 0.05
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (13 bp):
GGTCAACGTCAAA
Found at i:42916972 original size:27 final size:26
Alignment explanation
Indices: 42916941--42917002 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
42916931 AAAAGTTAAC
42916941 GGTCAAAGTCAACAGTCAACGATCAAA
1 GGTCAAAGTCAA-AGTCAACGATCAAA
* * *
42916968 GGTCAACTGTCAAAGTCAACGGTCAAC
1 GGTCAA-AGTCAAAGTCAACGATCAAA
42916995 GGTCAAAG
1 GGTCAAAG
42917003 GTAACGGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 1 0.03
27 24 0.80
28 5 0.17
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.16
Consensus pattern (26 bp):
GGTCAAAGTCAAAGTCAACGATCAAA
Found at i:42916986 original size:20 final size:20
Alignment explanation
Indices: 42916942--42917019 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
42916932 AAAGTTAACG
*
42916942 GTCAAA-GTCAACAGTCAAC
1 GTCAAAGGTCAACAGTCAAA
*
42916961 GATCAAAGGTCAACTGTCAAA
1 G-TCAAAGGTCAACAGTCAAA
* *
42916982 GTCAACGGTCAACGGTCAAA
1 GTCAAAGGTCAACAGTCAAA
*
42917002 GGT-AACGGTCAA-AGTCAA
1 -GTCAAAGGTCAACAGTCAA
42917020 CGGTCAACAG
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
19 6 0.12
20 31 0.61
21 14 0.27
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
GTCAAAGGTCAACAGTCAAA
Found at i:42917162 original size:26 final size:26
Alignment explanation
Indices: 42917133--42917197 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 26
42917123 TGGTTTAGGC
* **
42917133 TTAATGGGTTTTTTTTTTCTAAAGGG
1 TTAATGGGTTTTTGTTTTAAAAAGGG
* **
42917159 TTAA-GAGGCTTGGGTTTTAAAAAGGG
1 TTAATG-GGTTTTTGTTTTAAAAAGGG
42917185 TTAATGGGTTTTT
1 TTAATGGGTTTTT
42917198 AAAGAAATAA
Statistics
Matches: 28, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
25 1 0.04
26 26 0.93
27 1 0.04
ACGTcount: A:0.23, C:0.03, G:0.28, T:0.46
Consensus pattern (26 bp):
TTAATGGGTTTTTGTTTTAAAAAGGG
Found at i:42917574 original size:11 final size:11
Alignment explanation
Indices: 42917555--42917629 Score: 62
Period size: 12 Copynumber: 6.5 Consensus size: 11
42917545 AAGTGTGATC
*
42917555 AAAAAAGAAAG
1 AAAAGAGAAAG
42917566 AAAAGAGAAAAG
1 AAAAGAG-AAAG
42917578 AAAAGAGAAAG
1 AAAAGAGAAAG
42917589 AAATA-AGAAAG
1 AAA-AGAGAAAG
* * *
42917600 GAATGAAAAAAG
1 AAAAG-AGAAAG
*
42917612 GAAAGAGAAAGG
1 AAAAGAGAAA-G
42917624 AAAAGA
1 AAAAGA
42917630 TGAGAGGCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
11 25 0.48
12 27 0.52
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:42917581 original size:23 final size:23
Alignment explanation
Indices: 42917555--42917627 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
42917545 AAGTGTGATC
*
42917555 AAAAAAGAAAGAAAAGAGAAAAG
1 AAAAAAGAAAGAAAAGAGAAAGG
*
42917578 AAAAGAGAAAGAAATA-AGAAAGG
1 AAAAAAGAAAGAAA-AGAGAAAGG
* *
42917601 AATGAAA-AAAGGAAAGAGAAAGG
1 AA-AAAAGAAAGAAAAGAGAAAGG
42917624 AAAA
1 AAAA
42917628 GATGAGAGGC
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
22 2 0.05
23 36 0.88
24 3 0.07
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.03
Consensus pattern (23 bp):
AAAAAAGAAAGAAAAGAGAAAGG
Found at i:42919469 original size:18 final size:18
Alignment explanation
Indices: 42919446--42919481 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42919436 TAAAATGATG
42919446 AAGAAGAAGATGAAGAAA
1 AAGAAGAAGATGAAGAAA
* *
42919464 AAGAAGATGATGATGAAA
1 AAGAAGAAGATGAAGAAA
42919482 TTGAAAATTA
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:0.61, C:0.00, G:0.28, T:0.11
Consensus pattern (18 bp):
AAGAAGAAGATGAAGAAA
Found at i:42919526 original size:31 final size:30
Alignment explanation
Indices: 42919491--42919557 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 30
42919481 ATTGAAAATT
*
42919491 AAAATTA-TTTAATAATTTTATTATTTCAAAA
1 AAAATTATTTTAAGAATTTTA-TATTT-AAAA
*
42919522 AAAATAATTTTAAGAATTTTATATTTAAAA
1 AAAATTATTTTAAGAATTTTATATTTAAAA
*
42919552 ATAATT
1 AAAATT
42919558 TTAAAAAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 8 0.26
31 11 0.35
32 12 0.39
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (30 bp):
AAAATTATTTTAAGAATTTTATATTTAAAA
Found at i:42921311 original size:24 final size:24
Alignment explanation
Indices: 42921283--42921365 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
42921273 TAGACTAATA
42921283 AGAGTTTAACTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
** *
42921307 AGAGTTTATTTGAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
* *
42921331 AGAATTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
42921355 AAAGTTTAACT
1 AGAGTTTAACT
42921366 CGAAGATTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:42922981 original size:24 final size:25
Alignment explanation
Indices: 42922954--42923011 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
42922944 TAAACTAATA
* *
42922954 AGAGTTTAACTT-AAATAAGCAAAC
1 AGAGTTTAACTTGAAACAAACAAAC
* *
42922978 AGAGTTT-ATTTGAAACAAATAAAC
1 AGAGTTTAACTTGAAACAAACAAAC
42923002 AGAGTTTAAC
1 AGAGTTTAAC
42923012 CTCGAAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 3 0.11
24 23 0.85
25 1 0.04
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (25 bp):
AGAGTTTAACTTGAAACAAACAAAC
Found at i:42923962 original size:14 final size:14
Alignment explanation
Indices: 42923943--42923979 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
42923933 AGTAATTAAA
42923943 TTGTATTATTAATC
1 TTGTATTATTAATC
42923957 TTGTATTATTAATC
1 TTGTATTATTAATC
42923971 TTGTATTAT
1 TTGTATTAT
42923980 GCGTAAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.27, C:0.05, G:0.08, T:0.59
Consensus pattern (14 bp):
TTGTATTATTAATC
Found at i:42924657 original size:9 final size:9
Alignment explanation
Indices: 42924638--42924680 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
42924628 ATTAATGTAA
*
42924638 AATTAATAT
1 AATTAAAAT
42924647 AATTAAAAT
1 AATTAAAAT
42924656 AATTAAACAT
1 AATTAAA-AT
*
42924666 AATAAAAAT
1 AATTAAAAT
42924675 ATATTA
1 A-ATTA
42924681 TTTATAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
9 18 0.62
10 11 0.38
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
AATTAAAAT
Found at i:42924661 original size:18 final size:18
Alignment explanation
Indices: 42924638--42924680 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
42924628 ATTAATGTAA
* *
42924638 AATTAATATAATTAAAAT
1 AATTAACATAATAAAAAT
42924656 AATTAAACATAATAAAAAT
1 AATT-AACATAATAAAAAT
42924675 ATATTA
1 A-ATTA
42924681 TTTATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 4 0.19
19 14 0.67
20 3 0.14
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
AATTAACATAATAAAAAT
Found at i:42927097 original size:14 final size:14
Alignment explanation
Indices: 42927057--42927102 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
42927047 CAAAATTTTA
*
42927057 AAAATATAAAAAAT
1 AAAATATAAAAATT
*
42927071 AAAATTTACAAAATT
1 AAAATATA-AAAATT
*
42927086 AGAATATAAAAATT
1 AAAATATAAAAATT
42927100 AAA
1 AAA
42927103 CAACTTTTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:42928511 original size:12 final size:13
Alignment explanation
Indices: 42928486--42928514 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
42928476 AATTTGATTT
42928486 TTTAAAATTTTAA
1 TTTAAAATTTTAA
42928499 TTTAAAA-TTTAA
1 TTTAAAATTTTAA
42928511 TTTA
1 TTTA
42928515 TTAATTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTAAAATTTTAA
Found at i:42931297 original size:30 final size:31
Alignment explanation
Indices: 42931262--42931329 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
42931252 CTTAACTAAA
*
42931262 AAAAGTTATAATTT-AGTCATTGAATTATTC
1 AAAAGTTATAATTTAAGTCATTGAACTATTC
* * **
42931292 GAAAGTTTTCGTTTAAGTCATTGAACTATTC
1 AAAAGTTATAATTTAAGTCATTGAACTATTC
42931323 AAAAGTT
1 AAAAGTT
42931330 CTTACTTAGG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
30 10 0.32
31 21 0.68
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (31 bp):
AAAAGTTATAATTTAAGTCATTGAACTATTC
Found at i:42932699 original size:30 final size:30
Alignment explanation
Indices: 42932643--42932768 Score: 110
Period size: 27 Copynumber: 4.4 Consensus size: 30
42932633 AAAAATTAAA
*
42932643 TTCAACTTTTAAG-GGTTC--AA-TTTTTT
1 TTCAACTTTTAAGAGGTCCAAAATTTTTTT
*
42932669 TTCAATTTTTAAGAGGTCCAAAA-TTTTTT
1 TTCAACTTTTAAGAGGTCCAAAATTTTTTT
* *
42932698 TTCAGCTTTTAA-AGGGTCCAAAAATTATTTT
1 TTCAACTTTTAAGA-GGTCC-AAAATTTTTTT
*
42932729 ATCAACTTTTAAG-GG---ATAAATTTTTTT
1 TTCAACTTTTAAGAGGTCCA-AAATTTTTTT
42932756 TTCAACTTTTAAG
1 TTCAACTTTTAAG
42932769 GAATCCAAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
26 13 0.16
27 25 0.30
28 1 0.01
29 23 0.28
30 6 0.07
31 15 0.18
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (30 bp):
TTCAACTTTTAAGAGGTCCAAAATTTTTTT
Found at i:42932701 original size:29 final size:29
Alignment explanation
Indices: 42932643--42932768 Score: 122
Period size: 29 Copynumber: 4.4 Consensus size: 29
42932633 AAAAATTAAA
*
42932643 TTCAACTTTTAAG-GGTTC--AATTTTTT
1 TTCAACTTTTAAGAGGTCCAAAATTTTTT
*
42932669 TTCAATTTTTAAGAGGTCCAAAATTTTTT
1 TTCAACTTTTAAGAGGTCCAAAATTTTTT
*
42932698 TTCAGCTTTTAA-AGGGTCCAAAAATTATTTT
1 TTCAACTTTTAAGA-GGTCC-AAAATT-TTTT
* *
42932729 ATCAACTTTTAAG-GGAT--AAATTTTTTT
1 TTCAACTTTTAAGAGG-TCCAAAATTTTTT
42932756 TTCAACTTTTAAG
1 TTCAACTTTTAAG
42932769 GAATCCAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
26 12 0.14
27 20 0.24
28 6 0.07
29 23 0.27
30 8 0.10
31 15 0.18
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (29 bp):
TTCAACTTTTAAGAGGTCCAAAATTTTTT
Found at i:42949403 original size:19 final size:19
Alignment explanation
Indices: 42949376--42949421 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
42949366 TTGCCCTTGT
* * *
42949376 CCTTTCCCTTTCCCTTTCC
1 CCTTCCCCTTCCCCTTCCC
42949395 CCTTCCCCTTCCCCTTCCC
1 CCTTCCCCTTCCCCTTCCC
42949414 CCTCTCCC
1 CCT-TCCC
42949422 ACTCATCACC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (19 bp):
CCTTCCCCTTCCCCTTCCC
Found at i:42949416 original size:7 final size:6
Alignment explanation
Indices: 42949379--42949414 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
42949369 CCCTTGTCCT
* *
42949379 TTCCCT TTCCCT TTCCCC TTCCCC TTCCCC TTCCCC
1 TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC
42949415 CTCTCCCACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (6 bp):
TTCCCC
Found at i:42950516 original size:25 final size:23
Alignment explanation
Indices: 42950476--42950525 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
42950466 ATATATGATC
* *
42950476 CTTTTTTTATATAGTTTAGTCTT
1 CTTTTTTTAAATAGTTTAATCTT
42950499 CTTTTTTTAAAATAAGTTTAATCTT
1 CTTTTTTT-AAAT-AGTTTAATCTT
42950524 CT
1 CT
42950526 ACTTTATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
24 3 0.13
25 12 0.52
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.60
Consensus pattern (23 bp):
CTTTTTTTAAATAGTTTAATCTT
Found at i:42960449 original size:5 final size:5
Alignment explanation
Indices: 42960436--42960469 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
42960426 ACAGATTTAG
*
42960436 ATTGC ATTGT ATTGT ATTGT ATTGT ATTGT ATTG
1 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTG
42960470 AAACCATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.03, G:0.21, T:0.56
Consensus pattern (5 bp):
ATTGT
Found at i:42968209 original size:22 final size:21
Alignment explanation
Indices: 42968167--42968209 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
42968157 TCTCTTTTCT
*
42968167 TTTTTTCGTTTTCTTTATTTA
1 TTTTTTCGTTTTCCTTATTTA
*
42968188 TTTTTTCGATTTTCCTTCTTTA
1 TTTTTTCG-TTTTCCTTATTTA
42968210 GAATACAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.09, C:0.14, G:0.05, T:0.72
Consensus pattern (21 bp):
TTTTTTCGTTTTCCTTATTTA
Found at i:42976497 original size:3 final size:3
Alignment explanation
Indices: 42976489--42976526 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
42976479 AGTTTTAAAA
42976489 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
42976527 ATCCAATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:42978624 original size:28 final size:28
Alignment explanation
Indices: 42978580--42978740 Score: 143
Period size: 28 Copynumber: 5.9 Consensus size: 28
42978570 ATAGATAAGG
42978580 AATCA-ATATGCAAATTCATAGATACAA
1 AATCATATATGCAAATTCATAGATACAA
42978607 AATCATATATGCAAATTCATAGATA-AA
1 AATCATATATGCAAATTCATAGATACAA
* ** **
42978634 AA-AAT-TATGCTGATTCATA-AGTACGG
1 AATCATATATGCAAATTCATAGA-TACAA
* ** *
42978660 ATTCATATATGCGGATTTATAGATACAA
1 AATCATATATGCAAATTCATAGATACAA
* * *
42978688 ATTCATATATTCAGATTCATAGATACAA
1 AATCATATATGCAAATTCATAGATACAA
* * *
42978716 ATTCATATATGCAAGTACATAGATA
1 AATCATATATGCAAATTCATAGATA
42978741 GAGATTCATG
Statistics
Matches: 110, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
24 1 0.01
25 14 0.13
26 3 0.03
27 11 0.10
28 80 0.73
29 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (28 bp):
AATCATATATGCAAATTCATAGATACAA
Found at i:42978674 original size:14 final size:14
Alignment explanation
Indices: 42978645--42978725 Score: 65
Period size: 14 Copynumber: 5.8 Consensus size: 14
42978635 AAATTATGCT
*
42978645 GATTCATA-AGTACG
1 GATTCATATA-TACA
* *
42978659 GATTCATATATGCG
1 GATTCATATATACA
* *
42978673 GATTTATAGATACA
1 GATTCATATATACA
* *
42978687 AATTCATATATTCA
1 GATTCATATATACA
*
42978701 GATTCATAGATACA
1 GATTCATATATACA
*
42978715 AATTCATATAT
1 GATTCATATAT
42978726 GCAAGTACAT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
14 51 0.98
15 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (14 bp):
GATTCATATATACA
Found at i:42978888 original size:37 final size:37
Alignment explanation
Indices: 42978847--42978935 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
42978837 GAAACTTGGA
* ** *
42978847 GACAAGTTCAGTGGACTGTTTTAGCTTGAAACATGAG
1 GACAAGTTCAGTGGACCGCCTTAGCTTGAAACATAAG
* * * *
42978884 GACAAGTTTAGTCGACCGCCTTATCTTGAAATATAAG
1 GACAAGTTCAGTGGACCGCCTTAGCTTGAAACATAAG
42978921 GACAAGTTCAGTGGA
1 GACAAGTTCAGTGGA
42978936 ATATCTTAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (37 bp):
GACAAGTTCAGTGGACCGCCTTAGCTTGAAACATAAG
Found at i:42980853 original size:115 final size:115
Alignment explanation
Indices: 42980709--42980938 Score: 361
Period size: 115 Copynumber: 2.0 Consensus size: 115
42980699 AAATTATACT
*
42980709 TTCTTCGTGATGTTCAAAAGGAAGGAGAAGTGCAACTGGTTTATTACAATACATAAAATCAATAT
1 TTCTTCGTGATGTTCAAAAGGAAGGAGAAGTGCAACTGGTTTATTACAATACAGAAAATCAATAT
* * *
42980774 GCTGACGTTTCCACAAAAGCATTGCCTAAAGCTAGATTCGAGTTCTTAAG
66 GCTGACATTTCCACAAAAGCATTGCCTAAAGCCAGATTCAAGTTCTTAAG
* ** *
42980824 TTCTTCGTGATGTTCAAAAGGAAGGAGAAGTGCACCTGGTTTATTGTAGTACAGAAAATCAATAT
1 TTCTTCGTGATGTTCAAAAGGAAGGAGAAGTGCAACTGGTTTATTACAATACAGAAAATCAATAT
* * *
42980889 GCTGACATTTCCCCAAAAGCATTGCTTAAATCCAGATTCAAGTTCTTAAG
66 GCTGACATTTCCACAAAAGCATTGCCTAAAGCCAGATTCAAGTTCTTAAG
42980939 ACAAAAGCTT
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
115 104 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (115 bp):
TTCTTCGTGATGTTCAAAAGGAAGGAGAAGTGCAACTGGTTTATTACAATACAGAAAATCAATAT
GCTGACATTTCCACAAAAGCATTGCCTAAAGCCAGATTCAAGTTCTTAAG
Found at i:42981547 original size:1 final size:1
Alignment explanation
Indices: 42981541--42981565 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
42981531 CAAACTCATT
42981541 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
42981566 ATTTTTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:42981912 original size:17 final size:16
Alignment explanation
Indices: 42981877--42981930 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
42981867 ACATTTTATC
*
42981877 TTTAAAATAAT-TTTT
1 TTTAAAATAATATATT
42981892 TTTAAAATAATCATATT
1 TTTAAAATAAT-ATATT
**
42981909 TTTACATTTAATATATT
1 TTTA-AAATAATATATT
42981926 TTTAA
1 TTTAA
42981931 TTTTAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 11 0.33
16 1 0.03
17 16 0.48
18 5 0.15
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAAAATAATATATT
Found at i:42982515 original size:17 final size:17
Alignment explanation
Indices: 42982493--42982525 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42982483 TTTTTTACAA
42982493 ATTTT-AATACTTTTAAT
1 ATTTTAAATA-TTTTAAT
42982510 ATTTTAAATATTTTAA
1 ATTTTAAATATTTTAA
42982526 ACTACGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTAAATATTTTAAT
Found at i:42982624 original size:9 final size:9
Alignment explanation
Indices: 42982600--42982646 Score: 53
Period size: 8 Copynumber: 5.1 Consensus size: 9
42982590 TTATTTTAGA
42982600 TATACATTTT
1 TATA-ATTTT
42982610 TAATAATTTT
1 T-ATAATTTT
42982620 TATAATATTT
1 TATAAT-TTT
42982630 T-TAATTTT
1 TATAATTTT
42982638 TA-AATTTT
1 TATAATTTT
42982646 T
1 T
42982647 TAAATATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
8 11 0.32
9 9 0.26
10 11 0.32
11 3 0.09
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (9 bp):
TATAATTTT
Found at i:42982648 original size:16 final size:18
Alignment explanation
Indices: 42982613--42982649 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
42982603 ACATTTTTAA
42982613 TAATTTTTATAATATTTT
1 TAATTTTTATAATATTTT
42982631 TAATTTTTA-AAT-TTTT
1 TAATTTTTATAATATTTT
42982647 TAA
1 TAA
42982650 ATATATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 3 0.16
18 9 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TAATTTTTATAATATTTT
Found at i:42982660 original size:27 final size:28
Alignment explanation
Indices: 42982605--42982661 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
42982595 TTAGATATAC
*
42982605 ATTTTTAATAATTTTTATAATATTTTTA
1 ATTTTTAATAATTTTTATAATATTATTA
*
42982633 ATTTTTAA-ATTTTTTA-AATATATATTA
1 ATTTTTAATAATTTTTATAATAT-TATTA
42982660 AT
1 AT
42982662 GTCTATGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 5 0.19
27 13 0.50
28 8 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
ATTTTTAATAATTTTTATAATATTATTA
Found at i:42983158 original size:84 final size:85
Alignment explanation
Indices: 42982998--42983168 Score: 249
Period size: 86 Copynumber: 2.0 Consensus size: 85
42982988 TTCTAGTGAA
*
42982998 AAAAAAAAGATGATGTTCATCTTAAAAGATCCGATTTTCAACATCTGTTTGTGTGCGTTGTCAAA
1 AAAAAAAAGATGATGTTCATCTTAAAAGATCCGATTTTCAACACCTG-TTGTGTGCGTTGTCAAA
42983063 GAATTAAGAAAGTATGAACAG
65 GAATTAAGAAAGTATGAACAG
* * * *
42983084 AAAAAAAGGATGATGTTCATCTTAAGAGATCCGA-TTTCGAGCACCTG-TGTGTGTGTTGTCAAA
1 AAAAAAAAGATGATGTTCATCTTAAAAGATCCGATTTTC-AACACCTGTTGTGTGCGTTGTCAAA
42983147 TG-ATTAAGAAAGTATGAACAG
65 -GAATTAAGAAAGTATGAACAG
42983168 A
1 A
42983169 TATTATCATG
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
84 35 0.45
85 5 0.06
86 38 0.49
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (85 bp):
AAAAAAAAGATGATGTTCATCTTAAAAGATCCGATTTTCAACACCTGTTGTGTGCGTTGTCAAAG
AATTAAGAAAGTATGAACAG
Found at i:42985762 original size:12 final size:12
Alignment explanation
Indices: 42985747--42985783 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
42985737 ACAATTCATA
42985747 TCACTTTCAATT
1 TCACTTTCAATT
*
42985759 TCACTTTCATTT
1 TCACTTTCAATT
42985771 TCACTTTCAATT
1 TCACTTTCAATT
42985783 T
1 T
42985784 TGATCACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (12 bp):
TCACTTTCAATT
Found at i:42985958 original size:22 final size:22
Alignment explanation
Indices: 42985930--42985971 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
42985920 TAAACGTATA
42985930 ATATTTCACATATACATTGTTC
1 ATATTTCACATATACATTGTTC
42985952 ATATTTCACATATACATTGT
1 ATATTTCACATATACATTGT
42985972 CCATCACATA
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:0.33, C:0.17, G:0.05, T:0.45
Consensus pattern (22 bp):
ATATTTCACATATACATTGTTC
Found at i:42988386 original size:15 final size:15
Alignment explanation
Indices: 42988366--42988394 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42988356 GTTAATTTTC
42988366 AAAATTGTCCACTTG
1 AAAATTGTCCACTTG
42988381 AAAATTGTCCACTT
1 AAAATTGTCCACTT
42988395 CAGTCAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (15 bp):
AAAATTGTCCACTTG
Found at i:42997729 original size:16 final size:14
Alignment explanation
Indices: 42997710--42997743 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
42997700 AATAATTTTT
42997710 TTATAAATGTTATATA
1 TTATAAAT-TT-TATA
42997726 TTATAAATTTTATA
1 TTATAAATTTTATA
42997740 TTAT
1 TTAT
42997744 TTTTTACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 2 0.11
16 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
TTATAAATTTTATA
Found at i:43001106 original size:18 final size:18
Alignment explanation
Indices: 43001044--43001113 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
43001034 ATTATTCTAG
**
43001044 AATTTTTTTTAATTTTTT
1 AATTTTTTAAAATTTTTT
*
43001062 AACTTTCTTTATATATTTTTT
1 AA-TTT-TTTA-AAATTTTTT
*
43001083 AGATTTTTTAAAATTTTAT
1 A-ATTTTTTAAAATTTTTT
43001102 AATTTTTTAAAA
1 AATTTTTTAAAA
43001114 AATATAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 13 0.30
19 11 0.26
20 7 0.16
21 11 0.26
22 1 0.02
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (18 bp):
AATTTTTTAAAATTTTTT
Found at i:43001119 original size:17 final size:19
Alignment explanation
Indices: 43001085--43001125 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
43001075 TATTTTTTAG
**
43001085 ATTTTTTAAAATTTTAT-A
1 ATTTTTTAAAATAATATAA
43001103 ATTTTTTAAAA-AATATAA
1 ATTTTTTAAAATAATATAA
43001121 ATTTT
1 ATTTT
43001126 GATTTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTTTAAAATAATATAA
Found at i:43002079 original size:21 final size:21
Alignment explanation
Indices: 43002055--43002108 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
43002045 GTTGAGATGG
*
43002055 TTCTACCGATACAAGAG-TTAC
1 TTCTACCGATACAAG-GCATAC
* * *
43002076 TTCTACCTAAACAAGGCATGC
1 TTCTACCGATACAAGGCATAC
43002097 TTCTACCGATAC
1 TTCTACCGATAC
43002109 TAAAAACTCT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (21 bp):
TTCTACCGATACAAGGCATAC
Found at i:43002893 original size:42 final size:41
Alignment explanation
Indices: 43002803--43002945 Score: 135
Period size: 42 Copynumber: 3.4 Consensus size: 41
43002793 CCGAGCTATA
* * * *
43002803 AGTCTTCCTTTCAAACA-AATCTTATGCTCTACCGAGTCATA
1 AGTCTTCCTTT-AAACATAATCTCATGCTCTCCCGAGACATG
* *
43002844 AGTCTTCCTTTTAACATAATCTCATGCTCATCCCGAGACACG
1 AGTCTTCCTTTAAACATAATCTCATGCTC-TCCCGAGACATG
* * * *
43002886 AGTCTTCCTCTAAATATAATCTCATGCTTGTCCCGAAACATG
1 AGTCTTCCTTTAAACATAATCTCATGC-TCTCCCGAGACATG
* *
43002928 AGTCCTCCATTTATACAT
1 AGTCTTCC-TTTAAACAT
43002946 CAAGTGATTC
Statistics
Matches: 82, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
40 4 0.05
41 22 0.27
42 49 0.60
43 7 0.09
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (41 bp):
AGTCTTCCTTTAAACATAATCTCATGCTCTCCCGAGACATG
Found at i:43006973 original size:31 final size:31
Alignment explanation
Indices: 43006907--43006983 Score: 77
Period size: 31 Copynumber: 2.4 Consensus size: 31
43006897 TAAAATTTTA
43006907 AAAATATAATAATAAAATTACATTTTAATTCTT
1 AAAA-ATAATAA-AAAATTACATTTTAATTCTT
* *
43006940 AAAAGTAATAAAAAATTTA-A-TTTAATTTTTT
1 AAAAATAATAAAAAA-TTACATTTTAA-TTCTT
*
43006971 AAAAATTATAAAA
1 AAAAATAATAAAA
43006984 TATAAATAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
30 5 0.13
31 20 0.53
32 9 0.24
33 4 0.11
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (31 bp):
AAAAATAATAAAAAATTACATTTTAATTCTT
Found at i:43020709 original size:32 final size:33
Alignment explanation
Indices: 43020659--43020725 Score: 109
Period size: 32 Copynumber: 2.0 Consensus size: 33
43020649 ACAATTAAAA
*
43020659 TTTAAAATTTTTTATGAAAGAATAAATAATATTT
1 TTTAAAA-TTTTTATGAAAAAATAAATAATATTT
43020693 TTTAAAA-TTTTATGAAAAAATAAATAATATTT
1 TTTAAAATTTTTATGAAAAAATAAATAATATTT
43020725 T
1 T
43020726 ATCCTTCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 25 0.78
34 7 0.22
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (33 bp):
TTTAAAATTTTTATGAAAAAATAAATAATATTT
Found at i:43020826 original size:68 final size:68
Alignment explanation
Indices: 43020694--43020832 Score: 179
Period size: 68 Copynumber: 2.0 Consensus size: 68
43020684 ATAATATTTT
* * * **
43020694 TTAAAATTTTATGAAAAAATAAATAATATTTTATCCTTCAATTTATAACAATCAAAATGTTTAAA
1 TTAAAATTTTATGAAAAAATAAATAATATTTTATCCTTAAAATTAAAACAATCAAAATACTTAAA
*
43020759 GAA
66 AAA
** * * *
43020762 TTAAAATTTTATGAAAGGATAAATAATATTTTATTCTTAAAATTAAAACAGTTAAAATACTTAAA
1 TTAAAATTTTATGAAAAAATAAATAATATTTTATCCTTAAAATTAAAACAATCAAAATACTTAAA
43020827 AAA
66 AAA
43020830 TTA
1 TTA
43020833 TTTGTCCTTA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
68 60 1.00
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (68 bp):
TTAAAATTTTATGAAAAAATAAATAATATTTTATCCTTAAAATTAAAACAATCAAAATACTTAAA
AAA
Found at i:43030834 original size:33 final size:32
Alignment explanation
Indices: 43030771--43030837 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
43030761 ATTTAAGGAT
*
43030771 AAAATATTATTTATCTTTTTATAAAATTTTAA
1 AAAATATTATTTATCTTTTCATAAAATTTTAA
*
43030803 AAAATATTATTTAT-TCTTTCATAAAATTTTTA
1 AAAATATTATTTATCT-TTTCATAAAATTTTAA
43030835 AAA
1 AAA
43030838 TTTAAACTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 1 0.03
32 31 0.97
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (32 bp):
AAAATATTATTTATCTTTTCATAAAATTTTAA
Found at i:43033729 original size:24 final size:24
Alignment explanation
Indices: 43033697--43033751 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
43033687 AGAGGTAGCA
* *
43033697 GGAGCAGGAGTCGTTACTTTTTCC
1 GGAGGAGGAGTCATTACTTTTTCC
43033721 GGAGGAGGAGTCATTACTTTTTCC
1 GGAGGAGGAGTCATTACTTTTTCC
43033745 GGAGGAG
1 GGAGGAG
43033752 AGGTAGCTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.20, C:0.16, G:0.35, T:0.29
Consensus pattern (24 bp):
GGAGGAGGAGTCATTACTTTTTCC
Found at i:43034571 original size:24 final size:24
Alignment explanation
Indices: 43034541--43034595 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
43034531 CCAGCTACCT
*
43034541 CTCCTCCGGAAAAAGTAATGACTC
1 CTCCTCCGGAAAAAGTAACGACTC
43034565 CTCCTCCGGAAAAAGTAACGACTC
1 CTCCTCCGGAAAAAGTAACGACTC
*
43034589 CTGCTCC
1 CTCCTCC
43034596 TGCTACCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.35, G:0.16, T:0.20
Consensus pattern (24 bp):
CTCCTCCGGAAAAAGTAACGACTC
Found at i:43037490 original size:32 final size:32
Alignment explanation
Indices: 43037452--43037513 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
43037442 TTAAAATTTA
*
43037452 AAAATTTTATGAAATA-ATAAATAATATTTTTT
1 AAAATTTTAT-AAAAAGATAAATAATATTTTTT
43037484 AAAATTTTATAAAAAGATAAATAATATTTT
1 AAAATTTTATAAAAAGATAAATAATATTTT
43037514 ATCCTTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (32 bp):
AAAATTTTATAAAAAGATAAATAATATTTTTT
Found at i:43057815 original size:17 final size:17
Alignment explanation
Indices: 43057793--43057852 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
43057783 ACCTCGAACT
43057793 TTAAATATTTATCAAAC
1 TTAAATATTTATCAAAC
*
43057810 TTAAATATAATTACTC-AAG
1 TTAAATAT--TTA-TCAAAC
43057829 TCT-AATATTTATCAAAC
1 T-TAAATATTTATCAAAC
43057846 TTAAATA
1 TTAAATA
43057853 GAATTTTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
16 3 0.09
17 18 0.51
19 11 0.31
20 3 0.09
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.40
Consensus pattern (17 bp):
TTAAATATTTATCAAAC
Found at i:43058849 original size:15 final size:16
Alignment explanation
Indices: 43058796--43058851 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 16
43058786 ATTACCCATC
43058796 TCTTC-TAATTTTTTT
1 TCTTCATAATTTTTTT
*
43058811 TATT-ATAA--TTTTT
1 TCTTCATAATTTTTTT
43058824 TCTTCATAATTTTTTT
1 TCTTCATAATTTTTTT
*
43058840 TTTTCA-AATTTT
1 TCTTCATAATTTT
43058852 GACCTCTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
13 8 0.24
14 4 0.12
15 12 0.35
16 10 0.29
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (16 bp):
TCTTCATAATTTTTTT
Found at i:43058851 original size:14 final size:15
Alignment explanation
Indices: 43058801--43058851 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
43058791 CCATCTCTTC
43058801 TAATTTTTTTTATT-A
1 TAATTTTTTTT-TTCA
*
43058816 TAA-TTTTTTCTTCA
1 TAATTTTTTTTTTCA
43058830 TAATTTTTTTTTTTCA
1 TAA-TTTTTTTTTTCA
43058846 -AATTTT
1 TAATTTT
43058852 GACCTCTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
13 2 0.06
14 14 0.45
15 5 0.16
16 10 0.32
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (15 bp):
TAATTTTTTTTTTCA
Found at i:43061248 original size:30 final size:31
Alignment explanation
Indices: 43061201--43061258 Score: 109
Period size: 30 Copynumber: 1.9 Consensus size: 31
43061191 ATGATATTAT
43061201 TTTAACATTTAAAAAAATTAATAATAATTTA
1 TTTAACATTTAAAAAAATTAATAATAATTTA
43061232 TTTAACATTT-AAAAAATTAATAATAAT
1 TTTAACATTTAAAAAAATTAATAATAAT
43061259 CTGCCCTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (31 bp):
TTTAACATTTAAAAAAATTAATAATAATTTA
Found at i:43068904 original size:22 final size:22
Alignment explanation
Indices: 43068865--43068917 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
43068855 TTGAGAATTC
*
43068865 TTTTAGAATTTTTAATATATAT
1 TTTTAAAATTTTTAATATATAT
*
43068887 ATTTTAAAATTTTT-ATATATCT
1 -TTTTAAAATTTTTAATATATAT
43068909 TTTTAAAAT
1 TTTTAAAAT
43068918 AAAAAGTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 9 0.32
22 7 0.25
23 12 0.43
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTAAAATTTTTAATATATAT
Found at i:43070081 original size:23 final size:23
Alignment explanation
Indices: 43070055--43070113 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
43070045 TTATCTGTCT
43070055 TTATGGCACGCTTTTCCTCTACC
1 TTATGGCACGCTTTTCCTCTACC
** ***
43070078 TTATAACATATTTTTCCTCTACC
1 TTATGGCACGCTTTTCCTCTACC
*
43070101 TTGTGGCACGCTT
1 TTATGGCACGCTT
43070114 CTACCTTATG
Statistics
Matches: 25, Mismatches: 11, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.17, C:0.29, G:0.12, T:0.42
Consensus pattern (23 bp):
TTATGGCACGCTTTTCCTCTACC
Found at i:43071168 original size:14 final size:15
Alignment explanation
Indices: 43071131--43071183 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
43071121 TAGGGGTTTA
43071131 TTATA-TTATTAATTT
1 TTATATTTATT-ATTT
43071146 TTATCATTTATT-TTT
1 TTAT-ATTTATTATTT
*
43071161 TTATATTTATTATTA
1 TTATATTTATTATTT
43071176 TTATATTT
1 TTATATTT
43071184 TAAATGTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
14 7 0.21
15 21 0.62
16 1 0.03
17 5 0.15
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATATTTATTATTT
Found at i:43073530 original size:131 final size:130
Alignment explanation
Indices: 43073360--43073627 Score: 464
Period size: 131 Copynumber: 2.1 Consensus size: 130
43073350 TTAGAAATTG
* *
43073360 ACTTTACATGTAGAAAATGTAATGATTATCCTGAGATAAAATAAAATCATATTGGGAGAATGAAT
1 ACTTTTCATGTAGAAAATGTAATGATTACCCTGAGATAAAATAAAATCATATTGGGAGAATGAAT
*
43073425 TTATTCTAAATAGATAAGGATATCTTATGAGAGTAATACACTTATGACAAGGTCATTGGGCAAAC
66 TTATTCTAAATAGATAAGGATATCTTATGAGAGTAATACACTTATGACAAGGTCATTGGACAAAC
* *
43073490 ACTTTTCATGTAGGAAAATGTAATGATTACCCTGAGATAAAATATAATCATATTGGGAGAATGGA
1 ACTTTTCATGTA-GAAAATGTAATGATTACCCTGAGATAAAATAAAATCATATTGGGAGAATGAA
* *
43073555 TTTATTCTAAATAGATAAGGATATCTTATGAGAGTAATACACTTATGACAAGGTCATTTGACAAG
65 TTTATTCTAAATAGATAAGGATATCTTATGAGAGTAATACACTTATGACAAGGTCATTGGACAAA
43073620 C
130 C
43073621 ACTTTTC
1 ACTTTTC
43073628 GTAATGGTAT
Statistics
Matches: 130, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
130 11 0.08
131 119 0.92
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.32
Consensus pattern (130 bp):
ACTTTTCATGTAGAAAATGTAATGATTACCCTGAGATAAAATAAAATCATATTGGGAGAATGAAT
TTATTCTAAATAGATAAGGATATCTTATGAGAGTAATACACTTATGACAAGGTCATTGGACAAAC
Found at i:43074845 original size:23 final size:23
Alignment explanation
Indices: 43074815--43074858 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
43074805 TAAGTCCAAC
*
43074815 TGATGGATGAGGGACTGCAAAAT
1 TGATGGATGAGGAACTGCAAAAT
*
43074838 TGATGGATGAGGAATTGCAAA
1 TGATGGATGAGGAACTGCAAA
43074859 CCCTAATCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.34, T:0.23
Consensus pattern (23 bp):
TGATGGATGAGGAACTGCAAAAT
Found at i:43076084 original size:16 final size:17
Alignment explanation
Indices: 43076056--43076091 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
43076046 AATAAAAAAA
43076056 TTATTCATAATAAAATT
1 TTATTCATAATAAAATT
*
43076073 TTATTCAT-ATAAACTT
1 TTATTCATAATAAAATT
43076089 TTA
1 TTA
43076092 ATTTTATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATTCATAATAAAATT
Found at i:43077246 original size:32 final size:32
Alignment explanation
Indices: 43077207--43077267 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
43077197 TTGAATTATA
*
43077207 TTATTTTAACATTAAAAAAAAATAGTAATAAT
1 TTATTTTAACATTAAAAAAAAATAATAATAAT
* *
43077239 TTATTTTAACATTTAAAAATAATAATAAT
1 TTATTTTAACATTAAAAAAAAATAATAAT
43077268 CTGCCCTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (32 bp):
TTATTTTAACATTAAAAAAAAATAATAATAAT
Found at i:43077566 original size:12 final size:12
Alignment explanation
Indices: 43077549--43077574 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43077539 AATACATTTA
43077549 AAATATTAAAAC
1 AAATATTAAAAC
43077561 AAATATTAAAAC
1 AAATATTAAAAC
43077573 AA
1 AA
43077575 CAAACAAATT
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:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:43082772 original size:34 final size:34
Alignment explanation
Indices: 43082730--43082888 Score: 156
Period size: 34 Copynumber: 4.8 Consensus size: 34
43082720 AAAAATTTCT
*
43082730 ATTCATTCATATATTATAAACAATCAAGAATTTA
1 ATTCATTCATATATCATAAACAATCAAGAATTTA
* *
43082764 ATTTATTCATATATCACAAACAATCACA-AATTTTA
1 ATTCATTCATATATCATAAACAATCA-AGAA-TTTA
43082799 ATTCATTCATATATCAT-AA-AA--AA-AA-TTA
1 ATTCATTCATATATCATAAACAATCAAGAATTTA
* *
43082827 ATCCATTCATATATCATAAACAATCAAAGATTTTTA
1 ATTCATTCATATATCATAAACAATC-AAGA-ATTTA
* *
43082863 GTTCATTTATATAT--TAAACAATCAAG
1 ATTCATTCATATATCATAAACAATCAAG
43082889 TAAATAAAAC
Statistics
Matches: 105, Mismatches: 10, Indels: 21
0.77 0.07 0.15
Matches are distributed among these distances:
28 19 0.18
29 2 0.02
30 5 0.05
31 1 0.01
33 7 0.07
34 37 0.35
35 20 0.19
36 14 0.13
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.37
Consensus pattern (34 bp):
ATTCATTCATATATCATAAACAATCAAGAATTTA
Found at i:43085662 original size:15 final size:14
Alignment explanation
Indices: 43085637--43085672 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
43085627 AAAAAGTAAT
43085637 TAAAAAATTAAAAC
1 TAAAAAATTAAAAC
*
43085651 TCAAAAATTTAAAAC
1 T-AAAAAATTAAAAC
43085666 TAAAAAA
1 TAAAAAA
43085673 AATCTTATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAAAAATTAAAAC
Found at i:43086271 original size:12 final size:12
Alignment explanation
Indices: 43086230--43086304 Score: 50
Period size: 12 Copynumber: 6.6 Consensus size: 12
43086220 ACATCCAAAT
43086230 AACAAAAATAAC
1 AACAAAAATAAC
* * *
43086242 AACCAAAACAGC
1 AACAAAAATAAC
* *
43086254 AGCAAAAATAAT
1 AACAAAAATAAC
43086266 AAC---AA-AAC
1 AACAAAAATAAC
** *
43086274 AACATTAACAAC
1 AACAAAAATAAC
43086286 AACAAAAATAAC
1 AACAAAAATAAC
43086298 AACAAAA
1 AACAAAA
43086305 CAACAAAAAA
Statistics
Matches: 46, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
8 5 0.11
9 2 0.04
11 2 0.04
12 37 0.80
ACGTcount: A:0.69, C:0.20, G:0.03, T:0.08
Consensus pattern (12 bp):
AACAAAAATAAC
Found at i:43086306 original size:20 final size:20
Alignment explanation
Indices: 43086213--43086316 Score: 68
Period size: 20 Copynumber: 5.0 Consensus size: 20
43086203 AAAACACATA
* * *
43086213 AAAAATAACATCCAAATAAC
1 AAAAATAACAACAAAACAAC
43086233 AAAAATAACAACCAAAACAGCAGC
1 AAAAATAACAA-CAAAACA--A-C
*
43086257 AAAAATAATAACAAAACAAC
1 AAAAATAACAACAAAACAAC
** * *
43086277 ATTAACAACAACAAAAATAAC
1 AAAAATAACAAC-AAAACAAC
*
43086298 AACAA-AACAACAAAA-AAC
1 AAAAATAACAACAAAACAAC
43086316 A
1 A
43086317 GCAACCAAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
18 4 0.06
19 4 0.06
20 25 0.37
21 16 0.24
23 8 0.12
24 11 0.16
ACGTcount: A:0.69, C:0.20, G:0.02, T:0.09
Consensus pattern (20 bp):
AAAAATAACAACAAAACAAC
Found at i:43086325 original size:22 final size:20
Alignment explanation
Indices: 43086283--43086338 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 20
43086273 CAACATTAAC
43086283 AACAACAAAAATA-ACAACAA
1 AACAACAAAAA-ACACAACAA
43086303 AACAACAAAAAACAGCAACCAA
1 AACAACAAAAAACA-CAA-CAA
**
43086325 AACAGTAAAAAACA
1 AACAACAAAAAACA
43086339 ACACAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 12 0.39
21 3 0.10
22 15 0.48
ACGTcount: A:0.71, C:0.21, G:0.04, T:0.04
Consensus pattern (20 bp):
AACAACAAAAAACACAACAA
Found at i:43086345 original size:34 final size:34
Alignment explanation
Indices: 43086307--43086386 Score: 117
Period size: 34 Copynumber: 2.3 Consensus size: 34
43086297 CAACAAAACA
43086307 ACAAAAAACAGCAACCAAAACAGT-AAAAAACAAC
1 ACAAAAAACA-CAACCAAAACAGTAAAAAAACAAC
*
43086341 ACAAAAAAGACAACCAAAACAGTAAAAAAACAAC
1 ACAAAAAACACAACCAAAACAGTAAAAAAACAAC
43086375 ACCAAAACAACA
1 A-CAAAA-AACA
43086387 ATATAATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
33 13 0.32
34 20 0.49
35 5 0.12
36 3 0.07
ACGTcount: A:0.69, C:0.24, G:0.05, T:0.03
Consensus pattern (34 bp):
ACAAAAAACACAACCAAAACAGTAAAAAAACAAC
Found at i:43086355 original size:33 final size:34
Alignment explanation
Indices: 43086301--43086383 Score: 127
Period size: 33 Copynumber: 2.5 Consensus size: 34
43086291 AAATAACAAC
43086301 AAAACAACA-AAAAACAGCAACCAAAACAGT-AA
1 AAAACAACACAAAAACAGCAACCAAAACAGTAAA
43086333 AAAACAACACAAAAA-AGACAACCAAAACAGTAAA
1 AAAACAACACAAAAACAG-CAACCAAAACAGTAAA
*
43086367 AAAACAACACCAAAACA
1 AAAACAACACAAAAACA
43086384 ACAATATAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
32 11 0.24
33 18 0.39
34 16 0.35
35 1 0.02
ACGTcount: A:0.70, C:0.23, G:0.05, T:0.02
Consensus pattern (34 bp):
AAAACAACACAAAAACAGCAACCAAAACAGTAAA
Found at i:43088411 original size:21 final size:20
Alignment explanation
Indices: 43088353--43088412 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 20
43088343 ATTAAATAGT
43088353 TTTAAACAT-TATATGAAAAAA
1 TTTAAA-ATATATAT-AAAAAA
* *
43088374 ATTAAAAAAT-TATTAAAAAA
1 TTTAAAATATATA-TAAAAAA
43088394 CTTTAAAATATATATAAAA
1 -TTTAAAATATATATAAAA
43088413 TATAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
20 9 0.29
21 20 0.65
22 2 0.06
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (20 bp):
TTTAAAATATATATAAAAAA
Found at i:43088415 original size:9 final size:9
Alignment explanation
Indices: 43088397--43088438 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
43088387 TAAAAAACTT
43088397 TAAAATATA
1 TAAAATATA
43088406 TATAAA-ATA
1 TA-AAATATA
*
43088415 TAAAAAATA
1 TAAAATATA
43088424 TAAAATATAA
1 TAAAATAT-A
43088434 TAAAA
1 TAAAA
43088439 ATTGAAGTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 3 0.10
9 17 0.59
10 9 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
TAAAATATA
Found at i:43088426 original size:16 final size:17
Alignment explanation
Indices: 43088405--43088438 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
43088395 TTTAAAATAT
43088405 ATATAAAATATAA-AAA
1 ATATAAAATATAATAAA
43088421 ATATAAAATATAATAAA
1 ATATAAAATATAATAAA
43088438 A
1 A
43088439 ATTGAAGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
ATATAAAATATAATAAA
Found at i:43090689 original size:3 final size:3
Alignment explanation
Indices: 43090681--43090711 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
43090671 CCGGAGAGCA
43090681 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
43090712 GAGGGTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:43095428 original size:29 final size:29
Alignment explanation
Indices: 43095365--43095547 Score: 94
Period size: 29 Copynumber: 6.3 Consensus size: 29
43095355 GGAAAAAAAA
43095365 TAATTTTT-GACACTTCGAGGGTAAAACG
1 TAATTTTTGGACACTTCGAGGGTAAAACG
* *
43095393 GAGATTTTTGGACACTT-GAGGGTAAAATTG
1 TA-ATTTTTGGACACTTCGAGGGTAAAA-CG
** *
43095423 TAATTTTTGGA-TGTTC-AGGGTTAAAAACA
1 TAATTTTTGGACACTTCGAGGG-T-AAAACG
* * *
43095452 TAATTTTTGGAAAGTTCGA-AGTCAAAAATC-
1 TAATTTTTGGACACTTCGAGGGT--AAAA-CG
* * *
43095482 CAATTTTTGGACA-TACGAGGGTAAAATGG
1 TAATTTTTGGACACTTCGAGGGTAAAA-CG
* ** *
43095511 TAATTTTTAGA-TGTTCGAGGGTAAAAACA
1 TAATTTTTGGACACTTCGAGGGT-AAAACG
43095540 TAATTTTT
1 TAATTTTT
43095548 TGAAAGTTTG
Statistics
Matches: 121, Mismatches: 20, Indels: 27
0.72 0.12 0.16
Matches are distributed among these distances:
28 12 0.10
29 67 0.55
30 40 0.33
31 2 0.02
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (29 bp):
TAATTTTTGGACACTTCGAGGGTAAAACG
Found at i:43095502 original size:88 final size:87
Alignment explanation
Indices: 43095396--43095604 Score: 253
Period size: 88 Copynumber: 2.4 Consensus size: 87
43095386 TAAAACGGAG
* *
43095396 ATTTTTGGACACTTGAGGGTAAAATTGTAATTTTTGGATGTTC-AGGGTTAAAAACATAATTTTT
1 ATTTTTGGACA-TCGAGGGTAAAATTGTAATTTTTAGATGTTCGAGGG-TAAAAACATAATTTTT
43095460 GGAAAGTTCGAAGTCAAAAATCCA
64 GGAAAGTTCGAAGTCAAAAATCCA
* *
43095484 ATTTTTGGACATACGAGGGTAAAATGGTAATTTTTAGATGTTCGAGGGTAAAAACATAATTTTTT
1 ATTTTTGGACAT-CGAGGGTAAAATTGTAATTTTTAGATGTTCGAGGGTAAAAACATAATTTTTG
* ** **
43095549 GAAAGTTTGGGGTCAAAAATGGA
65 GAAAGTTCGAAGTCAAAAATCCA
* *
43095572 A-TTTTAGAAATTCGAGGGTAAAA-TGATAATTTT
1 ATTTTTGGACA-TCGAGGGTAAAATTG-TAATTTT
43095605 GGGAAGTTTG
Statistics
Matches: 105, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
86 1 0.01
87 26 0.25
88 74 0.70
89 4 0.04
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.35
Consensus pattern (87 bp):
ATTTTTGGACATCGAGGGTAAAATTGTAATTTTTAGATGTTCGAGGGTAAAAACATAATTTTTGG
AAAGTTCGAAGTCAAAAATCCA
Found at i:43095662 original size:57 final size:57
Alignment explanation
Indices: 43095540--43095784 Score: 234
Period size: 57 Copynumber: 4.3 Consensus size: 57
43095530 GGTAAAAACA
* * * * *
43095540 TAATTTTTTGAAAGTTTGGGGTCAAAAATGGAATTTTAGAAA-TTCGAGGGTAAAATGA
1 TAATTTTTGGAAAGTTTGAGGTCAAAAATGGAATTTTTGAAAGTT--TGGGTAAAATGG
*
43095598 TAA-TTTTGGGAAGTTTGAGGTCAAAAATGGAATTTTTGAAAGTTTGGGTAAAATGG
1 TAATTTTTGGAAAGTTTGAGGTCAAAAATGGAATTTTTGAAAGTTTGGGTAAAATGG
* * * *
43095654 TAATTTTTGGAAAG-TTGGGGTTAAAAATGGAATTTTTGAAAGTTTAGGGGAAAATTG
1 TAATTTTTGGAAAGTTTGAGGTCAAAAATGGAATTTTTGAAAGTTT-GGGTAAAATGG
* * * * *
43095711 TAATTTTT-AAGAAGTTTAAGGGCAAAAATGTAATTTTTGAGAA-ATTGGGTTCAAAGAT-G
1 TAATTTTTGGA-AAGTTTGAGGTCAAAAATGGAATTTTTGA-AAGTTTGGG-T-AAA-ATGG
43095770 TAA-TTTTGGAAAGTT
1 TAATTTTTGGAAAGTT
43095785 CAGGGGCAAA
Statistics
Matches: 157, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
56 43 0.27
57 66 0.42
58 36 0.23
59 10 0.06
60 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.36
Consensus pattern (57 bp):
TAATTTTTGGAAAGTTTGAGGTCAAAAATGGAATTTTTGAAAGTTTGGGTAAAATGG
Found at i:43095745 original size:30 final size:29
Alignment explanation
Indices: 43095504--43095818 Score: 151
Period size: 29 Copynumber: 10.9 Consensus size: 29
43095494 ATACGAGGGT
* * *
43095504 AAAATGGTAATTTTT-AGATGTTCGAGGGTA
1 AAAAT-GTAATTTTTGAGAAGTT-TAGGGCA
** *
43095534 AAAACATAATTTTTTGA-AAGTTTGGGGTCA
1 AAAATGTAA-TTTTTGAGAAGTTTAGGG-CA
* * * *
43095564 AAAATGGAA-TTTT-AGAAATTCGAGGG-T
1 AAAATGTAATTTTTGAGAAGTT-TAGGGCA
* *
43095591 AAAATGATAA-TTTTGGGAAGTTTGAGGTCA
1 AAAATG-TAATTTTTGAGAAGTTT-AGGGCA
* *
43095621 AAAATGGAATTTTTGA-AAGTTT-GGG-T
1 AAAATGTAATTTTTGAGAAGTTTAGGGCA
* *
43095647 AAAATGGTAATTTTTG-GAAAG-TTGGGGTTA
1 AAAAT-GTAATTTTTGAG-AAGTTTAGGG-CA
* *
43095677 AAAATGGAATTTTTGA-AAGTTTAGGGGA
1 AAAATGTAATTTTTGAGAAGTTTAGGGCA
* *
43095705 AAATTGTAATTTTTAAGAAGTTTAAGGGCA
1 AAAATGTAATTTTTGAGAAGTTT-AGGGCA
*
43095735 AAAATGTAATTTTTGAGAA-ATT-GGGTTCA
1 AAAATGTAATTTTTGAGAAGTTTAGGG--CA
* * *
43095764 AAGATGTAATTTTGGA-AAGTTCAGGGGC-
1 AAAATGTAATTTTTGAGAAGTTTA-GGGCA
*
43095792 AAAATGTAGTTTTTG-GAAAGTTTAGGG
1 AAAATGTAATTTTTGAG-AAGTTTAGGG
43095819 GTTAAAACAT
Statistics
Matches: 215, Mismatches: 43, Indels: 56
0.68 0.14 0.18
Matches are distributed among these distances:
26 5 0.02
27 23 0.11
28 54 0.25
29 71 0.33
30 58 0.27
31 4 0.02
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTTGAGAAGTTTAGGGCA
Found at i:43095886 original size:30 final size:30
Alignment explanation
Indices: 43095586--43095886 Score: 120
Period size: 30 Copynumber: 10.4 Consensus size: 30
43095576 TAGAAATTCG
* *
43095586 AGGGT-AAAATGATAA-TTTTGGGAAGTTTG
1 AGGGTGAAAATG-TAATTTTTGAGAAGTTTA
* *
43095615 A-GGTCAAAAATGGAATTTTTGA-AAGTTT-
1 AGGGT-GAAAATGTAATTTTTGAGAAGTTTA
43095643 -GGGT-AAAATGGTAATTTTTG-GAAAG-TT-
1 AGGGTGAAAAT-GTAATTTTTGAG-AAGTTTA
* * *
43095670 GGGGTTAAAAATGGAATTTTTGA-AAGTTT-
1 AGGG-TGAAAATGTAATTTTTGAGAAGTTTA
*
43095699 AGGG-GAAAATTGTAATTTTTAAGAAGTTTA
1 AGGGTGAAAA-TGTAATTTTTGAGAAGTTTA
** *
43095729 AGGGCAAAAATGTAATTTTTGAGAA-ATT-
1 AGGGTGAAAATGTAATTTTTGAGAAGTTTA
* * *
43095757 -GGGTTCAAAGATGTAATTTTGGA-AAG-TTC
1 AGGG-TGAAA-ATGTAATTTTTGAGAAGTTTA
*
43095786 AGGG-GCAAAATGTAGTTTTTG-GAAAGTTTA
1 AGGGTG-AAAATGTAATTTTTGAG-AAGTTTA
* * ** * * * **
43095816 GGGGTTAAAACATGATTTTCGAAAAGTTCG
1 AGGGTGAAAATGTAATTTTTGAGAAGTTTA
** * *
43095846 AGAATCAAAATGTAATTTTCGAGAAGTTTA
1 AGGGTGAAAATGTAATTTTTGAGAAGTTTA
43095876 AGGGTGAAAAT
1 AGGGTGAAAAT
43095887 ATGATTTCTA
Statistics
Matches: 204, Mismatches: 41, Indels: 53
0.68 0.14 0.18
Matches are distributed among these distances:
26 5 0.02
27 18 0.09
28 42 0.21
29 50 0.25
30 85 0.42
31 4 0.02
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (30 bp):
AGGGTGAAAATGTAATTTTTGAGAAGTTTA
Found at i:43097109 original size:11 final size:11
Alignment explanation
Indices: 43097084--43097124 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
43097074 TTAATAATAT
43097084 TATTTATTA-A
1 TATTTATTATA
43097094 TATTTATTATA
1 TATTTATTATA
43097105 TATTTATTATA
1 TATTTATTATA
43097116 TATTTATTA
1 TATTTATTA
43097125 AATACACAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 9 0.30
11 21 0.70
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTTATTATA
Found at i:43097120 original size:22 final size:23
Alignment explanation
Indices: 43097067--43097124 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 23
43097057 TTTCTTTTTA
* *
43097067 ATTAT-TATTAATAATATTATTT
1 ATTATATATTTATTATATTATTT
43097089 ATTA-ATATTTATTATA-TATTT
1 ATTATATATTTATTATATTATTT
43097110 ATTATATATTTATTA
1 ATTATATATTTATTA
43097125 AATACACAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 9 0.28
22 23 0.72
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTATATATTTATTATATTATTT
Found at i:43097844 original size:17 final size:17
Alignment explanation
Indices: 43097821--43097928 Score: 103
Period size: 17 Copynumber: 6.4 Consensus size: 17
43097811 GGCTTTCATC
*
43097821 ATTTAAATTTAGAATAA
1 ATTTAAATTTAAAATAA
* *
43097838 TTTTAAATTCAAAATAA
1 ATTTAAATTTAAAATAA
* * *
43097855 ATTTAAACTT-ATATTA
1 ATTTAAATTTAAAATAA
* *
43097871 ATTTAAACTTAAAACAA
1 ATTTAAATTTAAAATAA
*
43097888 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAAATAA
*
43097905 ACTT-AATCTTAAAATAA
1 ATTTAAAT-TTAAAATAA
43097922 ATTTAAA
1 ATTTAAA
43097929 AAATGAGTTT
Statistics
Matches: 71, Mismatches: 17, Indels: 5
0.76 0.18 0.05
Matches are distributed among these distances:
16 17 0.24
17 52 0.73
18 2 0.03
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.40
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:43097893 original size:50 final size:50
Alignment explanation
Indices: 43097821--43097915 Score: 118
Period size: 50 Copynumber: 1.9 Consensus size: 50
43097811 GGCTTTCATC
* * * * *
43097821 ATTTAAATTTAGAATAATTTTAAATTCAAAATAAATTTAAACTTATATTA
1 ATTTAAACTTAAAACAAATTTAAATTCAAAATAAACTTAAACTTATATTA
* * *
43097871 ATTTAAACTTAAAACAAATTTAAATTTAAAGTAAACTTAATCTTA
1 ATTTAAACTTAAAACAAATTTAAATTCAAAATAAACTTAAACTTA
43097916 AAATAAATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 37 1.00
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (50 bp):
ATTTAAACTTAAAACAAATTTAAATTCAAAATAAACTTAAACTTATATTA
Found at i:43098384 original size:86 final size:86
Alignment explanation
Indices: 43098234--43098403 Score: 279
Period size: 86 Copynumber: 2.0 Consensus size: 86
43098224 TGGTGTTATT
**
43098234 GATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCT
1 GATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTTCT
*
43098299 CTGTGTCTCATCAAGAAGACA
66 CTGTATCTCATCAAGAAGACA
*
43098320 GATTTGGT-TCACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTC
1 GATTTGGTCT-ACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTTC
*
43098384 TCTGTATCTCATCAGGAAGA
65 TCTGTATCTCATCAAGAAGA
43098404 TGACCGCATC
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
85 1 0.01
86 77 0.99
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.34
Consensus pattern (86 bp):
GATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTTCT
CTGTATCTCATCAAGAAGACA
Found at i:43098391 original size:49 final size:49
Alignment explanation
Indices: 43098331--43098452 Score: 226
Period size: 49 Copynumber: 2.5 Consensus size: 49
43098321 ATTTGGTTCA
*
43098331 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCG
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCG
43098380 CTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCG
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCG
*
43098429 CTTCTCTGTATCTCATCAAGAAGA
1 CTTCTCTGTATCTCATCAGGAAGA
43098453 CGAATTTAGT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 71 1.00
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.32
Consensus pattern (49 bp):
CTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCG
Found at i:43098487 original size:135 final size:135
Alignment explanation
Indices: 43098245--43098488 Score: 391
Period size: 135 Copynumber: 1.8 Consensus size: 135
43098235 ATTTGGTCTA
** *
43098245 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTTCTCTGTATCTCAT
* *
43098310 CAAGAAGACAGATTTGGTTCACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCA
66 CAAGAAGACAGATTTAGTCCACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCA
43098375 ATCCG
131 ATCCG
* *
43098380 CTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTTCTCTGTATCTCAT
* *
43098445 CAAGAAGAC-GAATTTAGTCCACTTCTTAGTATTTCATCAGGAAG
66 CAAGAAGACAG-ATTTAGTCCACTTCTCAGTATCTCATCAGGAAG
43098489 CTAACCATTT
Statistics
Matches: 99, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
134 1 0.01
135 98 0.99
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.33
Consensus pattern (135 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTTCTCTGTATCTCAT
CAAGAAGACAGATTTAGTCCACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCA
ATCCG
Found at i:43098748 original size:209 final size:208
Alignment explanation
Indices: 43098380--43098776 Score: 625
Period size: 209 Copynumber: 1.9 Consensus size: 208
43098370 TTTCAATCCG
* * *
43098380 CTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTTCTCTGTACCTCAT
* * *
43098445 CAAGAAGACGAATTTAGTCCACTTCTTAGTATTTCATCAGGAAGCTAACCATTTATTTGCTTCGA
66 CAAGAAGACGAACTTAGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTATTTGCTTCGA
* * * * *
43098510 CCTGCTTCTCAGTATCTCAACAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCTTGGGTTC
131 CCTGCTTCTCAGTATCTCAACAAGAAGCTGGGGTTAGAAG-GTTACCCACTTTGAGCTTGGGTTC
43098575 ATTGATTTGGTCTT
195 ATTGATTTGGTCTT
* *
43098589 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCTACTTCTTTGTACCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTTCTCTGTACCTCAT
* *
43098654 CAAGAAGACGAACTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCATTT-TATTGCTTCG
66 CAAGAAGACGAACTTAGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTAT-TTGCTTCG
*
43098718 ACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTAGAAGGTTACCCACTTTGAGCTT
130 ACCTGCTTCTCAGTATCTCAACAAGAAGCTGGGGTTAGAAGGTTACCCACTTTGAGCTT
43098777 TGAGTTGGTA
Statistics
Matches: 171, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
208 16 0.09
209 155 0.91
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (208 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCACTTCTCTGTACCTCAT
CAAGAAGACGAACTTAGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTATTTGCTTCGA
CCTGCTTCTCAGTATCTCAACAAGAAGCTGGGGTTAGAAGGTTACCCACTTTGAGCTTGGGTTCA
TTGATTTGGTCTT
Found at i:43110339 original size:28 final size:28
Alignment explanation
Indices: 43110284--43110481 Score: 144
Period size: 28 Copynumber: 7.0 Consensus size: 28
43110274 TTCGTATTGA
* *
43110284 GTAAAATGGAATTTTT-GAAAGTT-TGG
1 GTAAAATGTAATTTTTGGAAAGTTAGGG
43110310 GTAAAATGGTAATTTTTGGAAAGTT-GGG
1 GTAAAAT-GTAATTTTTGGAAAGTTAGGG
*
43110338 GTTAAAAATGGAATTTTT-GAAAGTTTAGGG
1 G-T-AAAATGTAATTTTTGGAAAG-TTAGGG
* ** *
43110368 G-AAAATGCAATTTTAAG-AAGTTTAAGG
1 GTAAAATGTAATTTTTGGAAAG-TTAGGG
*
43110395 GTAAAAATGTAATTTTTGAGAAA-TTTGGG
1 GT-AAAATGTAATTTTTG-GAAAGTTAGGG
43110424 GTCAAAGATGTAA-TTTTGGAAAGTTTAGGG
1 GT-AAA-ATGTAATTTTTGGAAAG-TTAGGG
* *
43110454 GCAAAATGT-AGTTTTGGAAAGTTTAGGG
1 GTAAAATGTAATTTTTGGAAAG-TTAGGG
43110482 TGTTAAAACA
Statistics
Matches: 143, Mismatches: 14, Indels: 28
0.77 0.08 0.15
Matches are distributed among these distances:
26 7 0.05
27 31 0.22
28 41 0.29
29 40 0.28
30 22 0.15
31 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.35
Consensus pattern (28 bp):
GTAAAATGTAATTTTTGGAAAGTTAGGG
Found at i:43110353 original size:29 final size:28
Alignment explanation
Indices: 43110286--43110448 Score: 124
Period size: 29 Copynumber: 5.8 Consensus size: 28
43110276 CGTATTGAGT
*
43110286 AAAATGGAATTTTT-GAAAGTTTGGGT-
1 AAAATGGAATTTTTGGAAAGTTGGGGTA
43110312 AAAATGGTAATTTTTGGAAAGTTGGGGTTA
1 AAAATGG-AATTTTTGGAAAGTTGGGG-TA
43110342 AAAATGGAATTTTT-GAAAGTTTAGGGG--
1 AAAATGGAATTTTTGGAAAG-TT-GGGGTA
* ** *
43110369 AAAATGCAATTTTAAG-AAGTTTAAGGGTA
1 AAAATGGAATTTTTGGAAAG-TT-GGGGTA
* *
43110398 AAAATGTAATTTTTGAGAAATTTGGGGTCA
1 AAAATGGAATTTTTG-GAAAGTTGGGGT-A
* *
43110428 AAGATGTAA-TTTTGGAAAGTT
1 AAAATGGAATTTTTGGAAAGTT
43110449 TAGGGGCAAA
Statistics
Matches: 114, Mismatches: 11, Indels: 22
0.78 0.07 0.15
Matches are distributed among these distances:
26 7 0.06
27 29 0.25
28 22 0.19
29 31 0.27
30 23 0.20
31 2 0.02
ACGTcount: A:0.37, C:0.01, G:0.26, T:0.36
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAAGTTGGGGTA
Found at i:43110482 original size:86 final size:83
Alignment explanation
Indices: 43110286--43110482 Score: 236
Period size: 86 Copynumber: 2.3 Consensus size: 83
43110276 CGTATTGAGT
* *
43110286 AAAATGGAATTTTTGAAAGTTT-GGGTAAAATGGTAATTTTTGGAAAGTTGGGGTTAAAAATGGA
1 AAAATGCAA-TTTTGAAAGTTTAGGGTAAAATGGTAATTTTTGGAAAGTTGGGGTCAAAAATGGA
*
43110350 ATTTTTGAAAGTTTAGGGG
65 ATTTTGGAAAGTTTAGGGG
* * *
43110369 AAAATGCAATTTTAAGAAGTTTAAGGGTAAAAAT-GTAATTTTTGAGAAATTTGGGGTCAAAGAT
1 AAAATGCAATTTTGA-AAGTTT-AGGGT-AAAATGGTAATTTTTG-GAAAGTTGGGGTCAAAAAT
*
43110433 GTAATTTTGGAAAGTTTAGGGG
62 GGAATTTTGGAAAGTTTAGGGG
* *
43110455 CAAAATGTAGTTTTGGAAAGTTTAGGGT
1 -AAAATGCAATTTT-GAAAGTTTAGGGT
43110483 GTTAAAACAT
Statistics
Matches: 97, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
82 5 0.05
83 14 0.14
85 14 0.14
86 46 0.47
87 17 0.18
88 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (83 bp):
AAAATGCAATTTTGAAAGTTTAGGGTAAAATGGTAATTTTTGGAAAGTTGGGGTCAAAAATGGAA
TTTTGGAAAGTTTAGGGG
Found at i:43111118 original size:29 final size:29
Alignment explanation
Indices: 43111054--43111120 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
43111044 TTTGGGTGCC
43111054 CGAGGGTAAAACAATAATTTTGGACACTTT
1 CGAGGGTAAAACAATAATTTTGGACAC-TT
*
43111084 TG-GGGTAAAACAATAAATTTTGGACAC-T
1 CGAGGGTAAAACAAT-AATTTTGGACACTT
43111112 CGAGGGTAA
1 CGAGGGTAA
43111121 TTTTGTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 2 0.06
29 18 0.55
30 13 0.39
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (29 bp):
CGAGGGTAAAACAATAATTTTGGACACTT
Found at i:43111189 original size:30 final size:29
Alignment explanation
Indices: 43111155--43111547 Score: 114
Period size: 29 Copynumber: 13.5 Consensus size: 29
43111145 GGTAAAAGCA
43111155 TAATTTGTGGAAAGTTCAGGGTCAAAAATG
1 TAATTT-TGGAAAGTTCAGGGTCAAAAATG
* *
43111185 TAATTTTTGGACA-TATAAGGGT--AAAATGG
1 TAA-TTTTGGAAAGT-TCAGGGTCAAAAAT-G
* * * **
43111214 TAATTTTAG-ATGTTCGAGGAT-AAAAACA
1 TAATTTTGGAAAGTTC-AGGGTCAAAAATG
*
43111242 TAATTTTTGGAAAGTTTAGGGTCAAAAATG
1 TAA-TTTTGGAAAGTTCAGGGTCAAAAATG
* * * * *
43111272 AAATTTTAGGAAAGTTTAAGGTTAAAAAATA
1 TAATTTT-GGAAAG-TTCAGGGTCAAAAATG
* *
43111303 AAATTTTTGG-AAGATTCGGGGGTCAAAAATG
1 TAA-TTTTGGAAAG-TTC-AGGGTCAAAAATG
* *
43111334 GAATTTTGGAAA-TTCGGGGGT--AAAATGG
1 TAATTTTGGAAAGTTC-AGGGTCAAAAAT-G
* *
43111362 TAATTTTTAGAAAGTTTAGGG---AAAATG
1 TAA-TTTTGGAAAGTTCAGGGTCAAAAATG
*
43111389 GAATTTTTGG-AAGTTC-GAGGT--AAAATGG
1 TAA-TTTTGGAAAGTTCAG-GGTCAAAAAT-G
** *
43111417 TAA-TTTGGAAAGTTTGGGGTTAAAAATAG
1 TAATTTTGGAAAGTTCAGGGTCAAAAAT-G
* *
43111446 -AATTTTTTG-AAGTT-AGAGGGCAAAAATG
1 TAA-TTTTGGAAAGTTCAG-GGTCAAAAATG
* * **
43111474 CAATTTT-GAGAAGTT-TGGGGGAAAAAGTG
1 TAATTTTGGA-AAGTTCAGGGTCAAAAA-TG
* *
43111503 TAATTTTTGAGAAA-TAT-GGGGTCAAAGATG
1 TAA-TTTTG-GAAAGT-TCAGGGTCAAAAATG
43111533 TAATTTTGGAAAGTT
1 TAATTTTGGAAAGTT
43111548 TGAGCTTAAA
Statistics
Matches: 279, Mismatches: 48, Indels: 74
0.70 0.12 0.18
Matches are distributed among these distances:
25 1 0.00
26 12 0.04
27 29 0.10
28 51 0.18
29 79 0.28
30 58 0.21
31 43 0.15
32 6 0.02
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (29 bp):
TAATTTTGGAAAGTTCAGGGTCAAAAATG
Found at i:43111307 original size:31 final size:30
Alignment explanation
Indices: 43111243--43111314 Score: 99
Period size: 31 Copynumber: 2.4 Consensus size: 30
43111233 ATAAAAACAT
* *
43111243 AATTTTTGGAAAGTTTAGGGTCAAAAATGA
1 AATTTTTGGAAAGTTTAGGGTAAAAAATAA
* *
43111273 AATTTTAGGAAAGTTTAAGGTTAAAAAATAA
1 AATTTTTGGAAAGTTT-AGGGTAAAAAATAA
43111304 AATTTTTGGAA
1 AATTTTTGGAA
43111315 GATTCGGGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 15 0.42
31 21 0.58
ACGTcount: A:0.44, C:0.01, G:0.19, T:0.35
Consensus pattern (30 bp):
AATTTTTGGAAAGTTTAGGGTAAAAAATAA
Found at i:43111413 original size:27 final size:29
Alignment explanation
Indices: 43111304--43111422 Score: 106
Period size: 27 Copynumber: 4.2 Consensus size: 29
43111294 TAAAAAATAA
*
43111304 AATTTTTGGAAGATTCGGGGGTCAAAAATGG-
1 AATTTTTGGAAG-TTCGGAGGT--AAAATGGT
* *
43111335 AA-TTTTGGAAATTCGGGGGTAAAATGGT
1 AATTTTTGGAAGTTCGGAGGTAAAATGGT
* * *
43111363 AATTTTTAGAAAGTT--TAGGGAAAATGG-
1 AATTTTT-GGAAGTTCGGAGGTAAAATGGT
43111390 AATTTTTGGAAGTTC-GAGGTAAAATGGT
1 AATTTTTGGAAGTTCGGAGGTAAAATGGT
43111418 AATTT
1 AATTT
43111423 GGAAAGTTTG
Statistics
Matches: 74, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
26 6 0.08
27 24 0.32
28 16 0.22
29 13 0.18
30 13 0.18
31 2 0.03
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (29 bp):
AATTTTTGGAAGTTCGGAGGTAAAATGGT
Found at i:43111627 original size:29 final size:30
Alignment explanation
Indices: 43111577--43111684 Score: 105
Period size: 29 Copynumber: 3.6 Consensus size: 30
43111567 TTGGAATGTT
** *
43111577 GTCAAAATATGATTTTCAAAAAGTTTGGGG
1 GTCAAAATATGATTTTTGAAAAGTTTAGGG
*
43111607 GT-AAAATATGATTTTTGAAAAGTTTAAGG
1 GTCAAAATATGATTTTTGAAAAGTTTAGGG
* * *
43111636 GTCAAAATGTAATTTTT-AAGAAG-TTCGGG
1 GTCAAAATATGATTTTTGAA-AAGTTTAGGG
*
43111665 GTGAAAATATGATTTCTTGA
1 GTCAAAATATGATTT-TTGA
43111685 TAGTTCAGGG
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
29 43 0.68
30 19 0.30
31 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.36
Consensus pattern (30 bp):
GTCAAAATATGATTTTTGAAAAGTTTAGGG
Found at i:43112893 original size:10 final size:10
Alignment explanation
Indices: 43112878--43112928 Score: 68
Period size: 10 Copynumber: 5.0 Consensus size: 10
43112868 TTAATAATAT
43112878 TATTTATTAA
1 TATTTATTAA
43112888 TATTTATTAA
1 TATTTATTAA
43112898 TA-TTATTATA
1 TATTTATTA-A
*
43112908 TATTTATTACT
1 TATTTATTA-A
43112919 TATTTATTAA
1 TATTTATTAA
43112929 ATACCACAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
9 6 0.17
10 15 0.42
11 15 0.42
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTTATTAA
Done.