Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 103 of 328
Found at i:28696129 original size:25 final size:26
Alignment explanation
Indices: 28696057--28696152 Score: 126
Period size: 26 Copynumber: 3.8 Consensus size: 26
28696047 CTCTTTTAAT
* *
28696057 AACTGGGGCAAAAGCCCTTTTTGATA
1 AACTGGGGCAAAAGCCCTTTTCGGTA
28696083 AACTGGGGCAAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAAGCCCTTTTCGGTA
*
28696109 AACTGGGGC-AAAGTCCTTTTCGGT-
1 AACTGGGGCAAAAGCCCTTTTCGGTA
* *
28696133 AACTAGGGC-ATAGCCCTTTT
1 AACTGGGGCAAAAGCCCTTTT
28696153 GCACTTCCTC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
24 17 0.27
25 14 0.22
26 33 0.52
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (26 bp):
AACTGGGGCAAAAGCCCTTTTCGGTA
Found at i:28702219 original size:25 final size:24
Alignment explanation
Indices: 28702173--28702220 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
28702163 GTAATATATT
*
28702173 TAAAATTAAAATATTTGTAATTTA
1 TAAAATTAAAATATCTGTAATTTA
28702197 TAAAATTCAAAATTATCTG-AATTT
1 TAAAATT-AAAA-TATCTGTAATTT
28702221 GTAAGAGCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 9 0.43
26 5 0.24
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (24 bp):
TAAAATTAAAATATCTGTAATTTA
Found at i:28703610 original size:6 final size:6
Alignment explanation
Indices: 28703550--28703619 Score: 54
Period size: 6 Copynumber: 11.2 Consensus size: 6
28703540 TTATAGTAAT
* *
28703550 AAAAG- AAAA-A AAAAGA CAAAAGCA AAACGA AACAGAA AGAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA -AAAAG-A AAAAGA AAAAG-A A-AAAGA AAAAGA
*
28703600 AAAAGA GAAAGA AAGAAGA A
1 AAAAGA AAAAGA AA-AAGA A
28703620 CCCACGGCTT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
5 8 0.15
6 22 0.42
7 18 0.35
8 4 0.08
ACGTcount: A:0.76, C:0.06, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:28706479 original size:16 final size:17
Alignment explanation
Indices: 28706453--28706484 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28706443 AAATTTTTAA
28706453 AAAAGAATAAAATAAAT
1 AAAAGAATAAAATAAAT
28706470 AAAA-AATAAAATAAA
1 AAAAGAATAAAATAAA
28706485 ATCTGATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (17 bp):
AAAAGAATAAAATAAAT
Found at i:28710507 original size:20 final size:20
Alignment explanation
Indices: 28710458--28710518 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
28710448 GTGAAAAGGG
28710458 AATTTTTG-AAGAACAATAA
1 AATTTTTGAAAGAACAATAA
** *
28710477 AATTTAGGAAAGAA-AGTCAA
1 AATTTTTGAAAGAACAAT-AA
*
28710497 AATTTTTGAAA-AAGAATAA
1 AATTTTTGAAAGAACAATAA
28710516 AAT
1 AAT
28710519 AAATAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.56, C:0.03, G:0.13, T:0.28
Consensus pattern (20 bp):
AATTTTTGAAAGAACAATAA
Found at i:28710532 original size:16 final size:17
Alignment explanation
Indices: 28710506--28710537 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28710496 AAATTTTTGA
28710506 AAAAGAATAAAATAAAT
1 AAAAGAATAAAATAAAT
28710523 AAAA-AATAAAATAAA
1 AAAAGAATAAAATAAA
28710538 ATTTGATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (17 bp):
AAAAGAATAAAATAAAT
Found at i:28721106 original size:3 final size:3
Alignment explanation
Indices: 28721098--28721132 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
28721088 AAAGAACACA
28721098 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
28721133 TGTAAATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:28722147 original size:20 final size:20
Alignment explanation
Indices: 28722122--28722159 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28722112 ACTTAGAGGG
28722122 ACTTCTATAC-ATACAAGTCC
1 ACTTCTAT-CGATACAAGTCC
28722142 ACTTCTATCGATACAAGT
1 ACTTCTATCGATACAAGT
28722160 TTGCTTCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (20 bp):
ACTTCTATCGATACAAGTCC
Found at i:28726038 original size:2 final size:2
Alignment explanation
Indices: 28726031--28726066 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28726021 TTGTGTTTTA
28726031 AT 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 AT
28726067 GAGATTTGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28734492 original size:20 final size:20
Alignment explanation
Indices: 28734467--28734504 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28734457 TGTTTAGGGC
28734467 AAAAATTTTCT-AAGTTTTGT
1 AAAAA-TTTCTAAAGTTTTGT
28734487 AAAAATTTCTAAAGTTTT
1 AAAAATTTCTAAAGTTTT
28734505 TGGTTTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (20 bp):
AAAAATTTCTAAAGTTTTGT
Found at i:28736377 original size:137 final size:137
Alignment explanation
Indices: 28736127--28736395 Score: 423
Period size: 137 Copynumber: 2.0 Consensus size: 137
28736117 CGATTTAGGG
**
28736127 ATGAAATATATGTGATTGAATGTTTTATGATATATTTAAATTAATGAATGTTATGATGTTTGAAT
1 ATGAAATATATGTGATTGAATGGCTTATGATATATTTAAATTAATGAATGTTATGATGTTTGAAT
* * *
28736192 ATTTCTAATTGTACGATAATACTCTGTAACCCTAATTCGACGATGGAGGCAGGTTAGGGGTGTTA
66 ATTTCTAATTGTACGATAATACTCCGTAACCCTAATCCGACGACGGAGGCAGGTTAGGGGTGTTA
28736257 CATTTAT
131 CATTTAT
* * *
28736264 ATGAAATGTATGTGATTGAATGGCTTATGATATATTTAAATTATTGAATGTTATGGTGTTTGAAT
1 ATGAAATATATGTGATTGAATGGCTTATGATATATTTAAATTAATGAATGTTATGATGTTTGAAT
* * *
28736329 ATTTTTTATTGTACGGTAATACTCCGTAACCCTAATCC-AGCGACGGAGGCAGGTTAGGGGTGTT
66 ATTTCTAATTGTACGATAATACTCCGTAACCCTAATCCGA-CGACGGAGGCAGGTTAGGGGTGTT
28736393 ACA
130 ACA
28736396 GTTCGAGTTT
Statistics
Matches: 120, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
136 1 0.01
137 119 0.99
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (137 bp):
ATGAAATATATGTGATTGAATGGCTTATGATATATTTAAATTAATGAATGTTATGATGTTTGAAT
ATTTCTAATTGTACGATAATACTCCGTAACCCTAATCCGACGACGGAGGCAGGTTAGGGGTGTTA
CATTTAT
Found at i:28738944 original size:16 final size:16
Alignment explanation
Indices: 28738912--28738947 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28738902 TTTGAAAGTT
**
28738912 TTTTTTTATAATTTAA
1 TTTTTTTATAAAATAA
28738928 TTTTTTTATAAAATAA
1 TTTTTTTATAAAATAA
28738944 TTTT
1 TTTT
28738948 AAATATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTTTATAAAATAA
Found at i:28739046 original size:23 final size:23
Alignment explanation
Indices: 28739020--28739063 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
28739010 TCAAATTGAC
28739020 TTTGATTCTACT-TATCAATAAAT
1 TTTGATTC-ACTATATCAATAAAT
*
28739043 TTTGATTCACTATGTCAATAA
1 TTTGATTCACTATATCAATAA
28739064 TTAAATCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (23 bp):
TTTGATTCACTATATCAATAAAT
Found at i:28739131 original size:31 final size:30
Alignment explanation
Indices: 28739096--28739178 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
28739086 TTAATGAGCT
*
28739096 AAATAAAAATATTTGAATAATTAAATAAGTA
1 AAATAAAAAT-TTTCAATAATTAAATAAGTA
* * *
28739127 AAATAAAAATTTTCAATAGTTTAATAATTA
1 AAATAAAAATTTTCAATAATTAAATAAGTA
* * *
28739157 AGATATAAATTTATTAATAATT
1 AAATAAAAATTT-TCAATAATT
28739179 TAAAGAGTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 26 0.60
31 17 0.40
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (30 bp):
AAATAAAAATTTTCAATAATTAAATAAGTA
Found at i:28742169 original size:25 final size:25
Alignment explanation
Indices: 28742141--28742192 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
28742131 TATTAACTAA
28742141 AGAACTGAACTTAAATAGAGAAAAG
1 AGAACTGAACTTAAATAGAGAAAAG
28742166 AGAACTGAACTTAAATAGAGAAAAG
1 AGAACTGAACTTAAATAGAGAAAAG
28742191 AG
1 AG
28742193 TCCTAATCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.56, C:0.08, G:0.21, T:0.15
Consensus pattern (25 bp):
AGAACTGAACTTAAATAGAGAAAAG
Found at i:28742271 original size:42 final size:42
Alignment explanation
Indices: 28742207--28742297 Score: 155
Period size: 42 Copynumber: 2.1 Consensus size: 42
28742197 AATCCTAATT
28742207 AGAACAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAA
1 AGAA-AATAGTTCCCTTATTCTAATAAACTACTAAAACATAAA
*
28742250 AGAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAA
1 AGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAA
*
28742292 ATAAAA
1 AGAAAA
28742298 ATATTCCTAG
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 42 0.91
43 4 0.09
ACGTcount: A:0.52, C:0.15, G:0.05, T:0.27
Consensus pattern (42 bp):
AGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAA
Found at i:28742318 original size:43 final size:42
Alignment explanation
Indices: 28742212--28742319 Score: 103
Period size: 42 Copynumber: 2.5 Consensus size: 42
28742202 TAATTAGAAC
* * * *
28742212 AATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAGAA
1 AATAGTTCCCTGAATATAATAAACTACTAAAACATAAAAAAA
* * * *
28742254 AATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAATAAA
1 AATAGTTCCCTGAATATAATAAACTACTAAAACATAAAA-AAA
28742297 AATA-TT-CCTAGAATATGAATAAA
1 AATAGTTCCCT-GAATAT-AATAAA
28742320 ACTTATTTAC
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
41 3 0.05
42 43 0.74
43 12 0.21
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.30
Consensus pattern (42 bp):
AATAGTTCCCTGAATATAATAAACTACTAAAACATAAAAAAA
Found at i:28742344 original size:19 final size:18
Alignment explanation
Indices: 28742322--28742361 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
28742312 TGAATAAAAC
*
28742322 TTATTTACCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
28742341 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
28742359 TTA
1 TTA
28742362 AAATATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:28746659 original size:42 final size:42
Alignment explanation
Indices: 28746600--28746688 Score: 160
Period size: 42 Copynumber: 2.1 Consensus size: 42
28746590 TCCTAATTAG
28746600 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
*
28746642 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
*
28746684 TAAAA
1 GAAAA
28746689 ATATTCCTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.28
Consensus pattern (42 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
Found at i:28746709 original size:43 final size:42
Alignment explanation
Indices: 28746601--28746710 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
28746591 CCTAATTAGG
* * * *
28746601 AAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAG
1 AAAATAGTTCCCTGAATATAATAAACTACTAAAACATAAAAA
* * * *
28746643 AAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAATA
1 AAAATAGTTCCCTGAATATAATAAACTACTAAAACATAAAA-A
28746686 AAAATA-TT-CCTAGAATATGAATAAA
1 AAAATAGTTCCCT-GAATAT-AATAAA
28746711 ACTTATTTAC
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
41 3 0.05
42 45 0.75
43 12 0.20
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (42 bp):
AAAATAGTTCCCTGAATATAATAAACTACTAAAACATAAAAA
Found at i:28746751 original size:18 final size:19
Alignment explanation
Indices: 28746713--28746752 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
28746703 TGAATAAAAC
*
28746713 TTATTTACCTAAATGAAAT
1 TTATCTACCTAAATGAAAT
28746732 TTATCTACCTAAAT-AAAT
1 TTATCTACCTAAATGAAAT
28746750 TTA
1 TTA
28746753 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (19 bp):
TTATCTACCTAAATGAAAT
Found at i:28758221 original size:36 final size:36
Alignment explanation
Indices: 28758174--28758248 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
28758164 CCTTGTCCAA
28758174 AAGCTGATGATATCATGATTTCTAGAGCCTCTCCTT
1 AAGCTGATGATATCATGATTTCTAGAGCCTCTCCTT
28758210 AAGCTGATGATATCATGATTTCTAGAGCCTCTCCTT
1 AAGCTGATGATATCATGATTTCTAGAGCCTCTCCTT
28758246 AAG
1 AAG
28758249 ATTCCATTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (36 bp):
AAGCTGATGATATCATGATTTCTAGAGCCTCTCCTT
Found at i:28770875 original size:15 final size:15
Alignment explanation
Indices: 28770836--28770864 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28770826 GACCACGACC
28770836 ATAGCCACCATGACT
1 ATAGCCACCATGACT
28770851 ATAGCCACCATGAC
1 ATAGCCACCATGAC
28770865 ATTGACCACC
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:0.34, G:0.14, T:0.17
Consensus pattern (15 bp):
ATAGCCACCATGACT
Found at i:28774479 original size:43 final size:43
Alignment explanation
Indices: 28774356--28774480 Score: 146
Period size: 43 Copynumber: 2.9 Consensus size: 43
28774346 TGATTACATG
* * *
28774356 TAAGACCATGTCTGGGACATTGGCATTG-TATTGTGATTACGTG
1 TAAGACCATGTCTGGGACATTGGCATCGATA-TGTGATTTCGTA
* *
28774399 TAAGACCATGTCTAGGACATTGGCATC-ATTATATGATTTCGTA
1 TAAGACCATGTCTGGGACATTGGCATCGA-TATGTGATTTCGTA
* * *
28774442 TAAGACCCTGTCTGGGATAGTGGCATCGATATGTGATTT
1 TAAGACCATGTCTGGGACATTGGCATCGATATGTGATTT
28774481 TCGAGTATCC
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
43 66 0.96
44 3 0.04
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (43 bp):
TAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTCGTA
Found at i:28776217 original size:18 final size:18
Alignment explanation
Indices: 28776180--28776218 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28776170 AAGTAGAGAA
*
28776180 AAATAAGGAAAATTGAGG
1 AAATAAGGAAAAATGAGG
28776198 AAATAAGGGAAAAATG-GG
1 AAATAA-GGAAAAATGAGG
28776216 AAA
1 AAA
28776219 ATAACAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.13
Consensus pattern (18 bp):
AAATAAGGAAAAATGAGG
Found at i:28776220 original size:19 final size:19
Alignment explanation
Indices: 28776179--28776222 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
28776169 CAAGTAGAGA
*
28776179 AAAATAAGGAAAATTGAGG
1 AAAATAAGGAAAAATGAGG
28776198 -AAATAAGGGAAAAATG-GG
1 AAAATAA-GGAAAAATGAGG
28776216 AAAATAA
1 AAAATAA
28776223 CAAAAATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (19 bp):
AAAATAAGGAAAAATGAGG
Found at i:28779072 original size:53 final size:53
Alignment explanation
Indices: 28779008--28779141 Score: 207
Period size: 53 Copynumber: 2.5 Consensus size: 53
28778998 TCATACCAAA
* *
28779008 GCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTATCACATTATACCGAT
1 GCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTATCACATTACACCGAT
* *
28779061 GCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTATCACATTGCACCGAT
1 GCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATTACACCGAT
*
28779114 GCCATAGCCCAGCTATGGTCTTAAACGG
1 GCCATAGCCCAGCTATGGTCTTATACGG
28779142 GCGCACTTAT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
52 1 0.01
53 74 0.99
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (53 bp):
GCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATTACACCGAT
Found at i:28786872 original size:12 final size:12
Alignment explanation
Indices: 28786855--28786890 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
28786845 CTGACCCGCC
28786855 TATATTAATTTT
1 TATATTAATTTT
28786867 TATATT-ATTTT
1 TATATTAATTTT
28786878 TATA-TAATTTT
1 TATATTAATTTT
28786889 TA
1 TA
28786891 AATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 16 0.70
12 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATATTAATTTT
Found at i:28789541 original size:39 final size:39
Alignment explanation
Indices: 28789459--28789611 Score: 234
Period size: 39 Copynumber: 3.9 Consensus size: 39
28789449 TATGGTAACC
* * *
28789459 CGCACAAATGCCTTCGGGACTTAACCCAGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
28789499 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
28789538 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
28789577 CTCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
28789612 TCGAACATTC
Statistics
Matches: 104, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 87 0.84
40 17 0.16
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:28804860 original size:59 final size:58
Alignment explanation
Indices: 28804736--28804886 Score: 153
Period size: 59 Copynumber: 2.6 Consensus size: 58
28804726 TTATATATTT
* * * *
28804736 TTTTTTTTTTAATTTAGCATCTAAACTATTTTTTACTCAATTTAGTACCCGAACTTGACA
1 TTTTTTTTCTAATTTAGTATCT-AACT-TTTTTTTCTCAATTTAGTACCCAAACTTGACA
* * * *
28804796 -CTTTTTTCTAATTTAGTATCTAA-TTTTTTTTCTCCCAATTTGGTACCTAAACTTGGCA
1 TTTTTTTTCTAATTTAGTATCTAACTTTTTTTTCT--CAATTTAGTACCCAAACTTGACA
* * *
28804854 TTTTTTTTCTAATTTGGTACCTAAGTTTTTTTT
1 TTTTTTTTCTAATTTAGTATCTAACTTTTTTTT
28804887 AGGTTCAATT
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
56 8 0.11
57 1 0.01
58 21 0.28
59 38 0.50
60 8 0.11
ACGTcount: A:0.23, C:0.16, G:0.08, T:0.53
Consensus pattern (58 bp):
TTTTTTTTCTAATTTAGTATCTAACTTTTTTTTCTCAATTTAGTACCCAAACTTGACA
Found at i:28805369 original size:61 final size:60
Alignment explanation
Indices: 28805257--28805370 Score: 149
Period size: 61 Copynumber: 1.9 Consensus size: 60
28805247 CCAAATTGAA
* *
28805257 CAAAAAATGTAAGTACCAAATTAGGAAAAAGAGTCAAGTTCATATACCAAATTGAACTCT
1 CAAAAAATGTAAGTACCAAATTAGAAAAAAGAGTCAAGTTCAGATACCAAATTGAACTCT
* * * *
28805317 CAAAAAGAT-TAAGTACCAACTTAAGAAAAAAGTGTCAAGTTTAGGTACCAAATT
1 CAAAAA-ATGTAAGTACCAAATT-AGAAAAAAGAGTCAAGTTCAGATACCAAATT
28805371 AGGAAAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 18 0.39
61 28 0.61
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (60 bp):
CAAAAAATGTAAGTACCAAATTAGAAAAAAGAGTCAAGTTCAGATACCAAATTGAACTCT
Found at i:28805389 original size:31 final size:30
Alignment explanation
Indices: 28805329--28805450 Score: 129
Period size: 31 Copynumber: 3.9 Consensus size: 30
28805319 AAAAGATTAA
*
28805329 GTACCAACTTAAGAAAAAAGTGTCAAGTTTAG
1 GTACCAAATTAAGAAAAAA-TGTCAAGTTT-G
*
28805361 GTACCAAATTAGGAAAAAATGT-ATAGTTTG
1 GTACCAAATTAAGAAAAAATGTCA-AGTTTG
*
28805391 AGTACCAAATTAAGAAAAACTGTCAAGTTTGG
1 -GTACCAAATTAAGAAAAAATGTCAAGTTT-G
* * * *
28805423 GTGCCAAATTAGGAAAAAGTATCAAGTT
1 GTACCAAATTAAGAAAAAATGTCAAGTT
28805451 CATATACCAA
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
30 2 0.03
31 57 0.73
32 19 0.24
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (30 bp):
GTACCAAATTAAGAAAAAATGTCAAGTTTG
Found at i:28806563 original size:82 final size:82
Alignment explanation
Indices: 28806426--28806576 Score: 275
Period size: 82 Copynumber: 1.8 Consensus size: 82
28806416 ACGAATTCTA
*
28806426 GAAAACATAACAAACAAAGTTCAAATGAATTTGTGAGCTACTAATATAACATACCATTTATGAAT
1 GAAAACATAACAAACAAAGTTCAAATGAATTAGTGAGCTACTAATATAACATACCATTTATGAAT
28806491 TTATGAATTTATACCTG
66 TTATGAATTTATACCTG
* *
28806508 GAAAACATAACAAACTAAGTTCAAATGAATTAGTGAGTTACTAATATAACATACCATTTATGAAT
1 GAAAACATAACAAACAAAGTTCAAATGAATTAGTGAGCTACTAATATAACATACCATTTATGAAT
28806573 TTAT
66 TTAT
28806577 AAGTTAGAAC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 66 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (82 bp):
GAAAACATAACAAACAAAGTTCAAATGAATTAGTGAGCTACTAATATAACATACCATTTATGAAT
TTATGAATTTATACCTG
Found at i:28810430 original size:29 final size:27
Alignment explanation
Indices: 28810391--28810445 Score: 65
Period size: 29 Copynumber: 2.0 Consensus size: 27
28810381 ATTTTAAAAA
* **
28810391 TTAAAAAAAAAATTGTAAAAATTATAT
1 TTAAAAAAAAAAGTAAAAAAATTATAT
28810418 TTAAAAAGTAAAAAGTAAAAAAATTATA
1 TTAAAAA--AAAAAGTAAAAAAATTATA
28810446 AAAAAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 7 0.30
29 16 0.70
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (27 bp):
TTAAAAAAAAAAGTAAAAAAATTATAT
Found at i:28810959 original size:6 final size:6
Alignment explanation
Indices: 28810941--28810972 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
28810931 CTTCAAATTA
28810941 TCCTTT ATCCTTT TCCTTT TCCTTT TCCTTT T
1 TCCTTT -TCCTTT TCCTTT TCCTTT TCCTTT T
28810973 ATGGTCTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (6 bp):
TCCTTT
Found at i:28816095 original size:21 final size:22
Alignment explanation
Indices: 28816047--28816097 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 22
28816037 TAACATAATT
28816047 TATTTT-A-AAATTTTTATTGA
1 TATTTTAACAAATTTTTATTGA
*
28816067 TGTTTTAACAAATTTTT-TT-A
1 TATTTTAACAAATTTTTATTGA
28816087 TATTATTAACA
1 TATT-TTAACA
28816098 CATAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 9 0.35
21 9 0.35
22 8 0.31
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (22 bp):
TATTTTAACAAATTTTTATTGA
Found at i:28816165 original size:21 final size:21
Alignment explanation
Indices: 28816127--28816166 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28816117 ACACTAAACT
28816127 TTAAACCTTAAATATTGAATC
1 TTAAACCTTAAATATTGAATC
* * *
28816148 TTAAATCTTGAATTTTGAA
1 TTAAACCTTAAATATTGAA
28816167 CTTGAATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (21 bp):
TTAAACCTTAAATATTGAATC
Found at i:28816172 original size:13 final size:13
Alignment explanation
Indices: 28816141--28816181 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
28816131 ACCTTAAATA
*
28816141 TTGAATCTTAAATC
1 TTGAATTTTAAA-C
*
28816155 TTGAATTTTGAAC
1 TTGAATTTTAAAC
28816168 TTGAATTTTAAAC
1 TTGAATTTTAAAC
28816181 T
1 T
28816182 CCAAACTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (13 bp):
TTGAATTTTAAAC
Found at i:28823081 original size:21 final size:20
Alignment explanation
Indices: 28823040--28823081 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
28823030 ACAATTGTAA
*
28823040 TTTCATTTATTAAACATTAT
1 TTTCATTTATAAAACATTAT
*
28823060 TTTCATTTAATAAAATATTAT
1 TTTCATTT-ATAAAACATTAT
28823081 T
1 T
28823082 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTCATTTATAAAACATTAT
Found at i:28824756 original size:2 final size:2
Alignment explanation
Indices: 28824749--28824794 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
28824739 TGTTATCTTT
*
28824749 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28824791 TA TA
1 TA TA
28824795 ATTATGGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28826988 original size:3 final size:3
Alignment explanation
Indices: 28826980--28827014 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
28826970 GGCTGAAGCT
* *
28826980 GAA GAA GAA GAA GAA GAA GAA GAA GGA GAT GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
28827015 GCTTGATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:28832121 original size:39 final size:39
Alignment explanation
Indices: 28832058--28832146 Score: 110
Period size: 38 Copynumber: 2.3 Consensus size: 39
28832048 TTGAAAGTAT
28832058 TTATATTAAAAAAATCAACCATAAATATAATAAATGTCTTA
1 TTATATTAAAAAAATCAA-CATAAATATAAT-AATGTCTTA
* *
28832099 TTATATTAAAAAACAT-AA-ATAAATATAATAATTTTTTA
1 TTATATTAAAAAA-ATCAACATAAATATAATAATGTCTTA
*
28832137 TTGTATTAAA
1 TTATATTAAA
28832147 TTTAATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
38 16 0.36
39 11 0.25
41 15 0.34
42 2 0.05
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (39 bp):
TTATATTAAAAAAATCAACATAAATATAATAATGTCTTA
Found at i:28833147 original size:7 final size:7
Alignment explanation
Indices: 28833135--28833173 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
28833125 AATAAAACGA
28833135 TTTTCTT
1 TTTTCTT
28833142 TTTTCTT
1 TTTTCTT
28833149 TTTTCTT
1 TTTTCTT
28833156 TTTTCTT
1 TTTTCTT
28833163 TTTTCTT
1 TTTTCTT
28833170 TTTT
1 TTTT
28833174 GTTTCATTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTCTT
Found at i:28836222 original size:6 final size:6
Alignment explanation
Indices: 28836200--28836270 Score: 90
Period size: 6 Copynumber: 11.7 Consensus size: 6
28836190 GTTAAATAAT
* * *
28836200 TATTATA TATATTA TTTTTA TTTTTA TTTTTA T-TTTA TATTTA TATTTA
1 TATT-TA TAT-TTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
28836249 TATTTA TATTTA TATTTA TATT
1 TATTTA TATTTA TATTTA TATT
28836271 AAATTACTAA
Statistics
Matches: 61, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
5 5 0.08
6 48 0.79
7 7 0.11
8 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TATTTA
Found at i:28837390 original size:47 final size:48
Alignment explanation
Indices: 28837295--28837421 Score: 136
Period size: 47 Copynumber: 2.7 Consensus size: 48
28837285 GTGCGAGTGA
* * * *
28837295 TACCTTGA-TTGGCTGTGGGCCATGGTATAGGTATTTTAGAGAGGAGT
1 TACCTTGATTTGGCTGTAGGCCATGGTATAGGTATATCAGAGAGAAGT
* * * *
28837342 TACCTTGATTTGGCTGTAGGCCATGTTATAGGTA-ATCCGGGATAAGT
1 TACCTTGATTTGGCTGTAGGCCATGGTATAGGTATATCAGAGAGAAGT
*
28837389 TACCTTGATTTGG-T-TAGGGCCTTGGTATAGGTA
1 TACCTTGATTTGGCTGTA-GGCCATGGTATAGGTA
28837422 CTTATCGATT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
45 2 0.03
46 15 0.22
47 28 0.41
48 23 0.34
ACGTcount: A:0.21, C:0.13, G:0.31, T:0.35
Consensus pattern (48 bp):
TACCTTGATTTGGCTGTAGGCCATGGTATAGGTATATCAGAGAGAAGT
Found at i:28844517 original size:48 final size:47
Alignment explanation
Indices: 28844450--28844578 Score: 143
Period size: 47 Copynumber: 2.7 Consensus size: 47
28844440 CGAGTGAGAT
* ** *
28844450 CTTGATTTGGATATAGGCCATGGTATAGGTATTTCAGAGAGGAA-TTAC
1 CTTGATTTGGCTACGGGCCATGGTATAGGTACTTC-GAGA-GAAGTTAC
* * *
28844498 CTTGATTTGGCTACGGGCCATGTTATAGGTACTTCGGGATAAGTTAC
1 CTTGATTTGGCTACGGGCCATGGTATAGGTACTTCGAGAGAAGTTAC
* * *
28844545 ATTGATTTGGCTACGGACCATAGTATAGGTACTT
1 CTTGATTTGGCTACGGGCCATGGTATAGGTACTT
28844579 ATCGATTGTG
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
46 2 0.03
47 37 0.54
48 30 0.43
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (47 bp):
CTTGATTTGGCTACGGGCCATGGTATAGGTACTTCGAGAGAAGTTAC
Found at i:28845960 original size:27 final size:26
Alignment explanation
Indices: 28845930--28845991 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
28845920 AGATAATTAA
28845930 AATAAAATCCTAAAT-TTGAATAATCCT
1 AATAAAAT-CTAAATATT-AATAATCCT
* * *
28845957 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTAAATATTAATAATCCT
28845984 AATAAAAT
1 AATAAAAT
28845992 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 23 0.79
28 4 0.14
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (26 bp):
AATAAAATCTAAATATTAATAATCCT
Found at i:28846567 original size:1 final size:1
Alignment explanation
Indices: 28846561--28846624 Score: 83
Period size: 1 Copynumber: 64.0 Consensus size: 1
28846551 TTAGTACTTA
* * * * *
28846561 TTTTTTTCTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTCTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28846625 ATTATTTATT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:28846585 original size:13 final size:13
Alignment explanation
Indices: 28846569--28846624 Score: 94
Period size: 13 Copynumber: 4.3 Consensus size: 13
28846559 TATTTTTTTC
28846569 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
*
28846582 TTTTTTTTTTTTT
1 TTTTTTTTTCTTT
28846595 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
*
28846608 TTTTTTTCTCTTT
1 TTTTTTTTTCTTT
28846621 TTTT
1 TTTT
28846625 ATTATTTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTTTTTTCTTT
Found at i:28846598 original size:26 final size:26
Alignment explanation
Indices: 28846561--28846624 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
28846551 TTAGTACTTA
*
28846561 TTTTTTTCTTTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTCTTTTTTTT
28846587 TTTTTTTTTTTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTCTTTTTTTT
* *
28846613 TTCTCTTTTTTT
1 TTTTTTTTTTTT
28846625 ATTATTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (26 bp):
TTTTTTTTTTTTTTTTTCTTTTTTTT
Found at i:28846837 original size:116 final size:116
Alignment explanation
Indices: 28846652--28846938 Score: 513
Period size: 116 Copynumber: 2.5 Consensus size: 116
28846642 GAATATATTA
* *
28846652 AACCTTTTAACGCGAAG-AGAGATGACAACCCAAGCACCCCACCCCGGTTACTCAGCCCAACATA
1 AACCTTTTGACGCGAAGTA-AAATGACAACCCAAGCACCCCACCCCGGTTACTCAGCCCAACATA
28846716 CTCCTAAAATTATTTATTTCCGGTTAGCGGAGTTTTACCCAACACGTCACAC
65 CTCCTAAAATTATTTATTTCCGGTTAGCGGAGTTTTACCCAACACGTCACAC
28846768 AACCTTTTGACGCGAAGTAAAATGACAACCCAAGCACCCCACCCCGGTTACTCAGCCCAACATAC
1 AACCTTTTGACGCGAAGTAAAATGACAACCCAAGCACCCCACCCCGGTTACTCAGCCCAACATAC
*
28846833 TCCTAAAATTATTTATTTCCGGTTAGCGGAGTTTTACCCAACACGTTACAC
66 TCCTAAAATTATTTATTTCCGGTTAGCGGAGTTTTACCCAACACGTCACAC
* *
28846884 AACCTTTTGACGCGAAGTAAAATGACAACCCAAGCACCCTACCCCGGTTATTCAG
1 AACCTTTTGACGCGAAGTAAAATGACAACCCAAGCACCCCACCCCGGTTACTCAG
28846939 TCAGTCACGA
Statistics
Matches: 165, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
116 164 0.99
117 1 0.01
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (116 bp):
AACCTTTTGACGCGAAGTAAAATGACAACCCAAGCACCCCACCCCGGTTACTCAGCCCAACATAC
TCCTAAAATTATTTATTTCCGGTTAGCGGAGTTTTACCCAACACGTCACAC
Found at i:28848973 original size:21 final size:21
Alignment explanation
Indices: 28848949--28848989 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
28848939 AAAGTGGTGT
28848949 TTGGCTGCAGGTGTAGGGTTG
1 TTGGCTGCAGGTGTAGGGTTG
28848970 TTGGCTGCAGGTGTAGGGTT
1 TTGGCTGCAGGTGTAGGGTT
28848990 ATTCTAGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.10, G:0.46, T:0.34
Consensus pattern (21 bp):
TTGGCTGCAGGTGTAGGGTTG
Found at i:28849166 original size:4 final size:5
Alignment explanation
Indices: 28849121--28849207 Score: 63
Period size: 6 Copynumber: 16.6 Consensus size: 5
28849111 GAATTTTATT
* * *
28849121 AATAT AATAA AAT-A ATTAA AA-ACA AACAA AATAA AATAA AAT-A AATAA
1 AATAA AATAA AATAA AATAA AATA-A AATAA AATAA AATAA AATAA AATAA
28849169 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA AAT
1 -AATAA -AATAA -AATAA -AATAA -AATAA -AATAA AAT
28849208 TTAAAATTAA
Statistics
Matches: 73, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
4 8 0.11
5 29 0.40
6 36 0.49
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (5 bp):
AATAA
Found at i:28849166 original size:9 final size:9
Alignment explanation
Indices: 28849121--28849207 Score: 56
Period size: 9 Copynumber: 9.3 Consensus size: 9
28849111 GAATTTTATT
28849121 AATATAATAA
1 AATA-AATAA
*
28849131 AATAATTAAA
1 AATAAAT-AA
* *
28849141 AACAAACAA
1 AATAAATAA
28849150 AATAAAATAA
1 AAT-AAATAA
28849160 AATAAATAA
1 AATAAATAA
28849169 TAAT-AATAA
1 -AATAAATAA
28849178 TAAT-AATAA
1 -AATAAATAA
28849187 TAAT-AATAA
1 -AATAAATAA
28849196 TAAT-AATAA
1 -AATAAATAA
28849205 AAT
1 AAT
28849208 TTAAAATTAA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
8 3 0.04
9 44 0.65
10 21 0.31
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (9 bp):
AATAAATAA
Found at i:28849172 original size:3 final size:3
Alignment explanation
Indices: 28849150--28849204 Score: 87
Period size: 3 Copynumber: 18.7 Consensus size: 3
28849140 AAACAAACAA
28849150 AAT AA- AAT AA- AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28849194 AAT AAT AAT AA
1 AAT AAT AAT AA
28849205 AATTTAAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.08
3 42 0.86
4 3 0.06
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:28849173 original size:15 final size:15
Alignment explanation
Indices: 28849124--28849207 Score: 86
Period size: 15 Copynumber: 5.7 Consensus size: 15
28849114 TTTTATTAAT
*
28849124 ATAATAAAATAATTA
1 ATAATAAAATAAATA
* *
28849139 AAAACAAACA-AAATA
1 ATAATAAA-ATAAATA
28849154 A-AATAAAATAAATA
1 ATAATAAAATAAATA
28849168 ATAATAATAAT-AATA
1 ATAATAA-AATAAATA
28849183 ATAATAATAAT-AATA
1 ATAATAA-AATAAATA
28849198 ATAATAAAAT
1 ATAATAAAAT
28849208 TTAAAATTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
13 1 0.02
14 14 0.23
15 42 0.69
16 4 0.07
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAATAAAATAAATA
Found at i:28855682 original size:27 final size:26
Alignment explanation
Indices: 28855652--28855713 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
28855642 AGATAATTAA
28855652 AATAAAATCCTAAAT-TTGAATAATCCT
1 AATAAAAT-CTAAATATT-AATAATCCT
* * *
28855679 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTAAATATTAATAATCCT
28855706 AATAAAAT
1 AATAAAAT
28855714 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 23 0.79
28 4 0.14
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (26 bp):
AATAAAATCTAAATATTAATAATCCT
Found at i:28857709 original size:19 final size:18
Alignment explanation
Indices: 28857682--28857718 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
28857672 TTAATTAAAG
28857682 GGTTAATTTTTTTAAAATT
1 GGTTAA-TTTTTTAAAATT
*
28857701 GGTTTATTTTTTAAAATT
1 GGTTAATTTTTTAAAATT
28857719 AATAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (18 bp):
GGTTAATTTTTTAAAATT
Found at i:28859242 original size:18 final size:18
Alignment explanation
Indices: 28859219--28859483 Score: 158
Period size: 18 Copynumber: 14.3 Consensus size: 18
28859209 GAATAATTAT
28859219 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAG
* * *
28859237 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAG
* * **
28859255 TTATTCAATAATAACCAG
1 TTATTCAGTAACAGTCAG
*
28859273 TTATTCAGTATCGATCAATTGATCGG
1 TTATTCAGTA---A-C-A--G-TCAG
* *
28859299 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* *
28859317 TTATTTAGTAA-AATCAG
1 TTATTCAGTAACAGTCAG
* * *
28859334 ATATTCAGTAACTATTAAG
1 TTATTCAGTAAC-AGTCAG
*
28859353 TTATTCAGTAGCAGTCA-
1 TTATTCAGTAACAGTCAG
* *
28859370 TTCATTCAGTGACAATCAG
1 TT-ATTCAGTAACAGTCAG
* *
28859389 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAG
28859407 TTATTCAGTAACAGTCTA-
1 TTATTCAGTAACAGTC-AG
* * *
28859425 ATATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* * *
28859443 TTATCCGGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* *
28859461 TTATTCAGTAATAATCAG
1 TTATTCAGTAACAGTCAG
28859479 TTATT
1 TTATT
28859484 TTACACCTTT
Statistics
Matches: 188, Mismatches: 45, Indels: 28
0.72 0.17 0.11
Matches are distributed among these distances:
17 16 0.09
18 138 0.73
19 18 0.10
21 2 0.01
22 1 0.01
23 2 0.01
26 11 0.06
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:28860758 original size:53 final size:53
Alignment explanation
Indices: 28860677--28860827 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
28860667 CTTACACGGT
* *
28860677 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
28860732 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
28860785 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
28860828 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:28868270 original size:53 final size:53
Alignment explanation
Indices: 28868189--28868339 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
28868179 CTTACACGGT
* *
28868189 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
28868244 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
28868297 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
28868340 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:28870075 original size:45 final size:45
Alignment explanation
Indices: 28869840--28870081 Score: 304
Period size: 45 Copynumber: 5.3 Consensus size: 45
28869830 ATCTAGAATA
* * *
28869840 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCG
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* * * * *
28869885 ATAACGGTAACAGTAACAATATTTGACACACAAAGTGTCGAATTG
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* *
28869930 GTAACGGTAACAGTAACAATATTCGACACACACAGTGCCGAATCG
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* * * **
28869975 GCAACGGTAACAGTAACAATATTCAACACACAAAGTGTTGAATCG
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* *
28870020 GTAAAACAGTAGCAGTAACAATATTCGACACACAAAGTGCCGAATCA
1 GT--AACAGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
*
28870067 GTAACAGTAGCAGTA
1 GTAACAGTAACAGTA
28870082 GCGGTAACAG
Statistics
Matches: 170, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
45 131 0.77
47 39 0.23
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.20
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
Found at i:28870285 original size:20 final size:21
Alignment explanation
Indices: 28870237--28870285 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
28870227 TACTTTTCAG
28870237 TTTTCAATTAATTCATATTTT
1 TTTTCAATTAATTCATATTTT
**
28870258 AATT-AATTAATT-ATATTTT
1 TTTTCAATTAATTCATATTTT
28870277 TTTTCAATT
1 TTTTCAATT
28870286 CAATATAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 9 0.39
20 12 0.52
21 2 0.09
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTCAATTAATTCATATTTT
Found at i:28871663 original size:4 final size:4
Alignment explanation
Indices: 28871654--28871684 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
28871644 CCTTTTCTCC
28871654 CTTT CTTT CTTT CTTT CTTT CCTTT CTTT CT
1 CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CT
28871685 CCCCTGTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
CTTT
Found at i:28871745 original size:9 final size:9
Alignment explanation
Indices: 28871727--28871761 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
28871717 TTTCTTTTTC
*
28871727 ATTTCTTTT
1 ATTTCATTT
28871736 ATTTCATTT
1 ATTTCATTT
28871745 ATTTC-TTT
1 ATTTCATTT
28871753 ATTTCATTT
1 ATTTCATTT
28871762 CTTTATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.71
Consensus pattern (9 bp):
ATTTCATTT
Found at i:28871753 original size:17 final size:18
Alignment explanation
Indices: 28871727--28871773 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
28871717 TTTCTTTTTC
28871727 ATTTCTTTTATTTCATTT
1 ATTTCTTTTATTTCATTT
28871745 ATTTC-TTTATTTCATTT
1 ATTTCTTTTATTTCATTT
* *
28871762 CTTTATTTTATT
1 ATTTCTTTTATT
28871774 ATTAAACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTCTTTTATTTCATTT
Found at i:28871763 original size:13 final size:13
Alignment explanation
Indices: 28871727--28871769 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
28871717 TTTCTTTTTC
* *
28871727 ATTTCTTTTATTT
1 ATTTCATTTCTTT
28871740 CATTT-ATTTCTTT
1 -ATTTCATTTCTTT
28871753 ATTTCATTTCTTT
1 ATTTCATTTCTTT
28871766 ATTT
1 ATTT
28871770 TATTATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 4 0.15
13 18 0.69
14 4 0.15
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTCATTTCTTT
Found at i:28872900 original size:25 final size:25
Alignment explanation
Indices: 28872872--28872920 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
28872862 GAATATATAT
*
28872872 ATATAATATTTTAATCATATTAAAA
1 ATATAATATTTTAATAATATTAAAA
*
28872897 ATATAATATTTTAATAATTTTAAA
1 ATATAATATTTTAATAATATTAAA
28872921 TATTTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
ATATAATATTTTAATAATATTAAAA
Found at i:28872917 original size:34 final size:34
Alignment explanation
Indices: 28872853--28872919 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 34
28872843 GATCATTTTA
*
28872853 CATATATAAGAATATATATATATAATATTTTAAT
1 CATATATAAAAATATATATATATAATATTTTAAT
*
28872887 CATAT-TAAAAATATA-ATATTTTAATAATTTTAA
1 CATATATAAAAATATATATA-TATAAT-ATTTTAA
28872920 ATATTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 3 0.10
33 14 0.48
34 12 0.41
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (34 bp):
CATATATAAAAATATATATATATAATATTTTAAT
Found at i:28872960 original size:13 final size:12
Alignment explanation
Indices: 28872908--28872957 Score: 61
Period size: 13 Copynumber: 4.2 Consensus size: 12
28872898 TATAATATTT
28872908 TAATAATTTT-A
1 TAATAATTTTAA
28872919 -AAT-ATTTTAA
1 TAATAATTTTAA
28872929 TAATAAATTTTAA
1 TAAT-AATTTTAA
28872942 GTAATAATTTTAA
1 -TAATAATTTTAA
28872955 TAA
1 TAA
28872958 ATATAAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 5 0.15
10 4 0.12
11 3 0.09
12 3 0.09
13 15 0.44
14 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (12 bp):
TAATAATTTTAA
Found at i:28879489 original size:15 final size:15
Alignment explanation
Indices: 28879469--28879501 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28879459 CTGAAGGTTA
28879469 ACTTGTTTTGAGAAT
1 ACTTGTTTTGAGAAT
*
28879484 ACTTGTTTTGAGAGT
1 ACTTGTTTTGAGAAT
28879499 ACT
1 ACT
28879502 AACTGATCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.45
Consensus pattern (15 bp):
ACTTGTTTTGAGAAT
Found at i:28884572 original size:14 final size:14
Alignment explanation
Indices: 28884553--28884582 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28884543 TTATATCGAG
28884553 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
28884567 ACCAATCCAATTCA
1 ACCAATCCAAATCA
28884581 AC
1 AC
28884583 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:28887267 original size:25 final size:27
Alignment explanation
Indices: 28887233--28887284 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
28887223 AATCGGTAAA
*
28887233 ATTTTTCTATCA-AT-ATTTTCATACG
1 ATTTTCCTATCATATAATTTTCATACG
28887258 ATTTTCCTATCATATCAATTTTCATAC
1 ATTTTCCTATCATAT-AATTTTCATAC
28887285 AAAAATATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 2 0.09
28 10 0.43
ACGTcount: A:0.29, C:0.19, G:0.02, T:0.50
Consensus pattern (27 bp):
ATTTTCCTATCATATAATTTTCATACG
Found at i:28900651 original size:29 final size:29
Alignment explanation
Indices: 28900610--28900667 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
28900600 CGGCTTGGAG
*
28900610 ACACACCCGTGTCCT-TGCCCGTATGGTTC
1 ACACACCCGTGTCCTCT-ACCGTATGGTTC
*
28900639 ACACGCCCGTGTCCTCTACCGTATGGTTC
1 ACACACCCGTGTCCTCTACCGTATGGTTC
28900668 CAAAACATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.14, C:0.38, G:0.21, T:0.28
Consensus pattern (29 bp):
ACACACCCGTGTCCTCTACCGTATGGTTC
Found at i:28903608 original size:21 final size:21
Alignment explanation
Indices: 28903570--28903634 Score: 80
Period size: 22 Copynumber: 3.1 Consensus size: 21
28903560 ACGGTGGTCG
*
28903570 AATTTTCTTTTTACAAAATCAA
1 AATTTTC-TTTTAAAAAATCAA
28903592 AATTTTCTTTTAAAAAAATCAA
1 AATTTTCTTTT-AAAAAATCAA
*
28903614 AACTTT-TTTT-AAAAATCAA
1 AATTTTCTTTTAAAAAATCAA
28903633 AA
1 AA
28903635 CTTTATTTCG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
19 11 0.28
21 8 0.20
22 21 0.52
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTTTCTTTTAAAAAATCAA
Found at i:28903621 original size:19 final size:19
Alignment explanation
Indices: 28903599--28903638 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
28903589 CAAAATTTTC
28903599 TTTTAAAAAAATCAAAACT
1 TTTTAAAAAAATCAAAACT
**
28903618 TTTTTTAAAAATCAAAACT
1 TTTTAAAAAAATCAAAACT
28903637 TT
1 TT
28903639 ATTTCGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTTAAAAAAATCAAAACT
Found at i:28903648 original size:19 final size:19
Alignment explanation
Indices: 28903605--28903642 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
28903595 TTTCTTTTAA
*
28903605 AAAAATCAAAACTTTTTTT
1 AAAAATCAAAACTTTATTT
28903624 AAAAATCAAAACTTTATTT
1 AAAAATCAAAACTTTATTT
28903643 CGAAATAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATCAAAACTTTATTT
Found at i:28903679 original size:22 final size:22
Alignment explanation
Indices: 28903654--28903701 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
28903644 GAAATAGTTG
*
28903654 AAAAAGATCAAAACTTTCTTTT
1 AAAAAGATCAAAACTTTCCTTT
** *
28903676 AAAAATTTTAAAACTTTCCTTT
1 AAAAAGATCAAAACTTTCCTTT
28903698 AAAA
1 AAAA
28903702 TGAGTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAAAGATCAAAACTTTCCTTT
Found at i:28903748 original size:52 final size:50
Alignment explanation
Indices: 28903672--28903902 Score: 140
Period size: 52 Copynumber: 4.6 Consensus size: 50
28903662 CAAAACTTTC
*
28903672 TTTTAAAAATTTTAAAAC-TTTCCTTTAAAATGAGTAAAAAAACAAATTTTTA
1 TTTTAAAAA-TCT-AAACTTTTCCTTTAAAAT-AGTAAAAAAACAAATTTTTA
* *
28903724 TTTTAAAAATCTAAACTTTCTCCTTTAAAA-A--AAAAGAATC-ACTATTTT-
1 TTTTAAAAATCTAAACTTT-TCCTTTAAAATAGTAAAA-AAACAAAT-TTTTA
* ** * * **
28903772 TCTTAAAAATC-AAAGCTTTTATTTTGAGATAGTTAAAAAAAATCAAAACTTTA
1 TTTTAAAAATCTAAA-CTTTTCCTTTAAAATAG-T-AAAAAAA-CAAATTTTTA
* * * *
28903825 -TTTAAAAATTTAAAC-TTTCCTTTGAAATGACTAAAAAAACATATTTTTA
1 TTTTAAAAATCTAAACTTTTCCTTTAAAAT-AGTAAAAAAACAAATTTTTA
* *
28903874 TTTTTAAAATCTAAA-ATTTCTCTTTAAAA
1 TTTTAAAAATCTAAACTTTTC-CTTTAAAA
28903903 AAAATCAAAA
Statistics
Matches: 137, Mismatches: 24, Indels: 37
0.69 0.12 0.19
Matches are distributed among these distances:
47 9 0.07
48 21 0.15
49 14 0.10
50 28 0.20
51 24 0.18
52 37 0.27
53 4 0.03
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.40
Consensus pattern (50 bp):
TTTTAAAAATCTAAACTTTTCCTTTAAAATAGTAAAAAAACAAATTTTTA
Found at i:28903860 original size:51 final size:50
Alignment explanation
Indices: 28903603--28903863 Score: 162
Period size: 52 Copynumber: 5.1 Consensus size: 50
28903593 ATTTTCTTTT
** * *
28903603 AAAAAAATCAAAACTTTTTTTAAAAATCAAAACTTT-ATTTCGAAATAGTTG
1 AAAAAAATCAAAACTTTTTTTAAAAATTTAAACTTTCCTTT-GAAATA-TTA
* * *
28903654 AAAAAGATCAAAACTTTCTTTTAAAAATTTTAAAACTTTCCTTTAAAATGAGT-
1 AAAAAAATCAAAACTTT-TTTTAAAAA-TTT-AAACTTTCCTTTGAAAT-ATTA
** *
28903707 AAAAAAA-CAAATTTTTATTTTAAAAATCTAAACTTTCTCCTTT-AAA-A--A
1 AAAAAAATCAAAACTTT-TTTTAAAAATTTAAAC-TT-TCCTTTGAAATATTA
* ** * ** *
28903755 AAAAGAATCACTA-TTTTTCTTAAAAA-TCAAAGCTTTTATTTTGAGATAGTTA
1 AAAAAAATCAAAACTTTTT-TTAAAAATTTAAA-C-TTTCCTTTGAAATA-TTA
* *
28903807 AAAAAAATCAAAACTTTATTTAAAAATTTAAACTTTCCTTTGAAATGACTA
1 AAAAAAATCAAAACTTTTTTTAAAAATTTAAACTTTCCTTTGAAAT-ATTA
28903858 AAAAAA
1 AAAAAA
28903864 CATATTTTTA
Statistics
Matches: 162, Mismatches: 29, Indels: 38
0.71 0.13 0.17
Matches are distributed among these distances:
47 9 0.06
48 22 0.14
49 4 0.02
50 4 0.02
51 41 0.25
52 51 0.31
53 15 0.09
54 12 0.07
55 4 0.02
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (50 bp):
AAAAAAATCAAAACTTTTTTTAAAAATTTAAACTTTCCTTTGAAATATTA
Found at i:28903871 original size:150 final size:150
Alignment explanation
Indices: 28903617--28903906 Score: 433
Period size: 150 Copynumber: 1.9 Consensus size: 150
28903607 AAATCAAAAC
* * *
28903617 TTTTTTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAGATCAAAACTTTCTTTTAAAAAT
1 TTTTTTTAAAAATCAAAACTTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTCATTTAAAAAT
* *
28903682 TTTAAAACTTTCCTTTAAAATGAGTAAAAAAACAAATTTTTATTTTAAAAATCTAAACTTTCTCC
66 TTTAAAACTTTCCTTTAAAATGACTAAAAAAACAAATTTTTATTTTAAAAATCTAAAATTTCT-C
28903747 TTTAAAAAAAAAGAATCACTA
130 TTTAAAAAAAAAGAATCACTA
* * *
28903768 TTTTTCTTAAAAATCAAAGCTTTTATTTTGAGATAGTTAAAAAAAATCAAAACTTT-ATTTAAAA
1 TTTTT-TTAAAAATCAAAAC-TTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTCATTTAAAA
* * *
28903832 A-TTT-AAACTTTCCTTTGAAATGACTAAAAAAACATATTTTTATTTTTAAAATCTAAAATTTCT
64 ATTTTAAAACTTTCCTTTAAAATGACTAAAAAAACAAATTTTTATTTTAAAAATCTAAAATTTCT
28903895 CTTTAAAAAAAA
129 CTTTAAAAAAAA
28903907 TCAAAACTTT
Statistics
Matches: 126, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
149 12 0.10
150 54 0.43
151 8 0.06
152 21 0.17
153 31 0.25
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.39
Consensus pattern (150 bp):
TTTTTTTAAAAATCAAAACTTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTCATTTAAAAAT
TTTAAAACTTTCCTTTAAAATGACTAAAAAAACAAATTTTTATTTTAAAAATCTAAAATTTCTCT
TTAAAAAAAAAGAATCACTA
Found at i:28903942 original size:150 final size:151
Alignment explanation
Indices: 28903570--28903922 Score: 417
Period size: 150 Copynumber: 2.4 Consensus size: 151
28903560 ACGGTGGTCG
* **
28903570 AATTTTCT-TTTTACAAAATC-AAAATTT-T-CTTT-TAAAAA-AATCAAAACTTTTTTTAAAAA
1 AATTTT-TATTTTA-AAAATCTAAAATTTCTCCTTTAAAAAAAGAATCAAAACTTTTCCTAAAAA
* * * *
28903629 TCAAAAC-TTTATTTCGAAATAGTTGAAAAAGATCAAAACTTTCTTTTAAAAATTTTAAAACTTT
64 TCAAAGCTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTCATTTAAAAATTTTAAAACTTT
*
28903693 CCTTTAAAATGAGTAAAAAAACA
129 CCTTTAAAATGACTAAAAAAACA
* ** * *
28903716 AATTTTTATTTTAAAAATCTAAACTTTCTCCTTTAAAAAAAAAGAATCACTATTTTTCTTAAAAA
1 AATTTTTATTTTAAAAATCTAAAATTTCTCCTTT--AAAAAAAGAATCAAAACTTTTCCTAAAAA
* *
28903781 TCAAAGCTTTTATTTTGAGATAGTTAAAAAAAATCAAAACTTT-ATTTAAAAA-TTT-AAACTTT
64 TCAAAGCTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTCATTTAAAAATTTTAAAACTTT
*
28903843 CCTTTGAAATGACTAAAAAAACA
129 CCTTTAAAATGACTAAAAAAACA
* *
28903866 TATTTTTATTTTTAAAATCTAAAATTTCT-CTTT-AAAAAA-AATCAAAACTTTTCCTAA
1 AATTTTTATTTTAAAAATCTAAAATTTCTCCTTTAAAAAAAGAATCAAAACTTTTCCTAA
28903923 GATTAAGCCT
Statistics
Matches: 177, Mismatches: 21, Indels: 19
0.82 0.10 0.09
Matches are distributed among these distances:
145 21 0.12
146 23 0.13
147 1 0.01
148 4 0.02
149 4 0.02
150 54 0.31
151 8 0.05
152 31 0.18
153 31 0.18
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (151 bp):
AATTTTTATTTTAAAAATCTAAAATTTCTCCTTTAAAAAAAGAATCAAAACTTTTCCTAAAAATC
AAAGCTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTTTCATTTAAAAATTTTAAAACTTTCC
TTTAAAATGACTAAAAAAACA
Found at i:28904115 original size:9 final size:9
Alignment explanation
Indices: 28904065--28904120 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 9
28904055 TGTATAAGGC
28904065 AAAAAA-AA
1 AAAAAAGAA
28904073 AAAAAA-AA
1 AAAAAAGAA
28904081 AAAAAAGAA
1 AAAAAAGAA
* *
28904090 GAAGAAGAA
1 AAAAAAGAA
28904099 GAAGAAAAGAAA
1 -AA-AAAAG-AA
28904111 AAAAAAGAA
1 AAAAAAGAA
28904120 A
1 A
28904121 CTATAATGCT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 14 0.35
9 12 0.30
10 6 0.15
11 6 0.15
12 2 0.05
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:28904272 original size:12 final size:12
Alignment explanation
Indices: 28904252--28904285 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
28904242 TAATAACATT
*
28904252 TAATAATAATGG
1 TAATAATAATGA
*
28904264 TAGTAATAATGA
1 TAATAATAATGA
28904276 TAATAATAAT
1 TAATAATAAT
28904286 AATTTGCGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (12 bp):
TAATAATAATGA
Found at i:28905227 original size:10 final size:10
Alignment explanation
Indices: 28905214--28905248 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
28905204 CTTTTATCTT
*
28905214 TCTTTAATTA
1 TCTTTATTTA
28905224 TCTTTATTTA
1 TCTTTATTTA
*
28905234 TCTGTATTTA
1 TCTTTATTTA
28905244 TCTTT
1 TCTTT
28905249 TAGAATTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.20, C:0.11, G:0.03, T:0.66
Consensus pattern (10 bp):
TCTTTATTTA
Found at i:28906019 original size:40 final size:38
Alignment explanation
Indices: 28905973--28906050 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 38
28905963 CGGAATTTCA
*
28905973 ATCAAAACTTTTAATTCTGTTTTTATTTTATTTTTTCCAG
1 ATCAAAACTTTTAATTCTGTTTTT-TTAT-TTTTTTCCAG
28906013 ATCAAAACTTTTAATTCTGTTTTTTTATTTTTTTCCAG
1 ATCAAAACTTTTAATTCTGTTTTTTTATTTTTTTCCAG
28906051 GTACGCAGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
38 10 0.27
39 3 0.08
40 24 0.65
ACGTcount: A:0.24, C:0.13, G:0.05, T:0.58
Consensus pattern (38 bp):
ATCAAAACTTTTAATTCTGTTTTTTTATTTTTTTCCAG
Found at i:28907384 original size:3 final size:3
Alignment explanation
Indices: 28907376--28907412 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
28907366 AGAAATTTAC
28907376 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28907413 GTCATATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28912430 original size:20 final size:19
Alignment explanation
Indices: 28912392--28912431 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28912382 TATTATTATT
*
28912392 TTTTATCATTTCAATTCAA
1 TTTTATCATTTCAAATCAA
*
28912411 TTTTATCATTTATAAATCAA
1 TTTTATCATTT-CAAATCAA
28912431 T
1 T
28912432 GTATTTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTATCATTTCAAATCAA
Found at i:28913633 original size:24 final size:24
Alignment explanation
Indices: 28913606--28913654 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
28913596 TCAAAATTAA
28913606 CTAAAAAGGACTTAATTGACTTAC
1 CTAAAAAGGACTTAATTGACTTAC
28913630 CTAAAAAGGACTTAATTGACTTAC
1 CTAAAAAGGACTTAATTGACTTAC
28913654 C
1 C
28913655 AAATTAACTC
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:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (24 bp):
CTAAAAAGGACTTAATTGACTTAC
Found at i:28914085 original size:33 final size:33
Alignment explanation
Indices: 28914043--28914114 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
28914033 TTTACACATG
* *
28914043 TATATTTTTATTACCATACAATTATCTACTATT
1 TATATTTTTATTACCACACAATTATCTACCATT
28914076 TATATTTTTATTACCACACAATTATCTACCATT
1 TATATTTTTATTACCACACAATTATCTACCATT
28914109 TA-ATTT
1 TATATTT
28914115 ATTTAATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
32 4 0.11
33 33 0.89
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (33 bp):
TATATTTTTATTACCACACAATTATCTACCATT
Found at i:28916504 original size:29 final size:29
Alignment explanation
Indices: 28916462--28916536 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
28916452 GAAATATTTT
*
28916462 CATGGCCCGAAGCCAAAACATCTGATATG
1 CATGGCCCAAAGCCAAAACATCTGATATG
*
28916491 CATGGCCCAAAGCCAAAACATTTGATATG
1 CATGGCCCAAAGCCAAAACATCTGATATG
*
28916520 CATGGCCCAAAGTCAAA
1 CATGGCCCAAAGCCAAA
28916537 TCAGTATAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (29 bp):
CATGGCCCAAAGCCAAAACATCTGATATG
Found at i:28918819 original size:19 final size:20
Alignment explanation
Indices: 28918788--28918826 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
28918778 CCTTCTCTTC
28918788 CCTTTCTTTTTCC-TTTTCT
1 CCTTTCTTTTTCCATTTTCT
28918807 CCTTT-TTTCTTCCATTTTCT
1 CCTTTCTTT-TTCCATTTTCT
28918827 TCCCTACCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 9 0.50
20 6 0.33
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.67
Consensus pattern (20 bp):
CCTTTCTTTTTCCATTTTCT
Found at i:28920657 original size:6 final size:6
Alignment explanation
Indices: 28920646--28920716 Score: 108
Period size: 6 Copynumber: 11.7 Consensus size: 6
28920636 AGTCCCTTAA
28920646 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
*
28920693 TTTTAT TTTCTCT TATTTAT TTTT
1 TTTTAT TTT-TAT T-TTTAT TTTT
28920717 GAAGACTTAT
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
5 5 0.08
6 47 0.78
7 6 0.10
8 2 0.03
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:28921728 original size:4 final size:4
Alignment explanation
Indices: 28921721--28921795 Score: 150
Period size: 4 Copynumber: 18.8 Consensus size: 4
28921711 CTTAAAAAAA
28921721 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
28921769 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
28921796 TTAGTAGTAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 71 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:28925051 original size:21 final size:23
Alignment explanation
Indices: 28925004--28925057 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
28924994 CATTCAAGAT
**
28925004 AAAATAATATATAAAACTCTTTA
1 AAAATAATATATAAAACTAATTA
*
28925027 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTA
28925048 AAAAT-ATATA
1 AAAATAATATA
28925058 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:28925286 original size:15 final size:15
Alignment explanation
Indices: 28925266--28925311 Score: 74
Period size: 15 Copynumber: 2.9 Consensus size: 15
28925256 ATATAAATAG
28925266 AAATAGAAATATAAT
1 AAATAGAAATATAAT
28925281 AAATAGAAATATAAT
1 AAATAGAAATATAAT
28925296 AATAGTAGAAATATAA
1 AA-A-TAGAAATATAA
28925312 ATAGATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 17 0.59
16 1 0.03
17 11 0.38
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (15 bp):
AAATAGAAATATAAT
Found at i:28925299 original size:29 final size:28
Alignment explanation
Indices: 28925258--28925340 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 28
28925248 ATATTAGTAT
28925258 ATAAATAGAAATAGA-AATATAATAAATAG
1 ATAAATA-AAATAGAGAA-ATAATAAATAG
28925287 A-AATATAATAATAGTAGAAAT-ATAAATAG
1 ATAA-ATAA-AATAG-AGAAATAATAAATAG
*
28925316 ATAAATAAAATTAGATAAATAATAA
1 ATAAATAAAA-TAGAGAAATAATAA
28925341 TAGTATTAGA
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
28 10 0.22
29 29 0.63
30 5 0.11
31 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (28 bp):
ATAAATAAAATAGAGAAATAATAAATAG
Found at i:28925337 original size:14 final size:13
Alignment explanation
Indices: 28925258--28925343 Score: 59
Period size: 14 Copynumber: 6.0 Consensus size: 13
28925248 ATATTAGTAT
28925258 ATAAATAGAAATAG
1 ATAAATA-AAATAG
28925272 A-AATATAATAAATAG
1 ATAA-AT-A-AAATAG
28925287 A-AATATAATAATAG
1 ATAA-ATAA-AATAG
*
28925301 TAGAAATATAAATAG
1 -ATAAATA-AAATAG
28925316 ATAAATAAAATTAG
1 ATAAATAAAA-TAG
28925330 ATAAATAATAATAG
1 ATAAATAA-AATAG
28925344 TATTAGAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
13 6 0.10
14 29 0.47
15 24 0.39
16 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (13 bp):
ATAAATAAAATAG
Found at i:28925351 original size:46 final size:45
Alignment explanation
Indices: 28925233--28925351 Score: 124
Period size: 44 Copynumber: 2.7 Consensus size: 45
28925223 TATATAAAAA
* *
28925233 ATAAT-AAT-GAAAATAATATTAGTATATAAATAGAAATAGAAAT
1 ATAATAAATAGAAAATAATAATAGTATAGAAATAGAAATAGAAAT
*
28925276 ATAATAAATAGAAATATAATAATAG--TAGAAATATAAATAGATAA-
1 ATAATAAATAGAAA-ATAATAATAGTATAGAAATAGAAATAGA-AAT
*
28925320 ATAA-AATTAGATAAATAATAATAGTATTAGAA
1 ATAATAAATAGA-AAATAATAATAGTA-TAGAA
28925352 TAACAAAATA
Statistics
Matches: 64, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
43 21 0.33
44 23 0.36
45 6 0.09
46 14 0.22
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.29
Consensus pattern (45 bp):
ATAATAAATAGAAAATAATAATAGTATAGAAATAGAAATAGAAAT
Found at i:28928685 original size:18 final size:18
Alignment explanation
Indices: 28928644--28928679 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28928634 ACAGTGGGTG
28928644 AAATTAGGTTTTCAAGTC
1 AAATTAGGTTTTCAAGTC
28928662 AAATTAGGTTTTCAAGTC
1 AAATTAGGTTTTCAAGTC
28928680 TTATTAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (18 bp):
AAATTAGGTTTTCAAGTC
Found at i:28942030 original size:16 final size:17
Alignment explanation
Indices: 28941996--28942030 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28941986 GTTTTGTCCA
*
28941996 TTTATGGTTTTGGACTT
1 TTTATGGTTTTGAACTT
28942013 TTTATGGTTTT-AACTT
1 TTTATGGTTTTGAACTT
28942029 TT
1 TT
28942031 CTAATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.14, C:0.06, G:0.17, T:0.63
Consensus pattern (17 bp):
TTTATGGTTTTGAACTT
Found at i:28943401 original size:3 final size:3
Alignment explanation
Indices: 28943393--28943421 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28943383 GCACATTTTG
28943393 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28943422 GTTGTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28946953 original size:27 final size:27
Alignment explanation
Indices: 28946901--28946953 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
28946891 TTTTAGTTTT
* * *
28946901 TTTATATATTTATATATATAATTTTAA
1 TTTATATATTCATATATACAAATTTAA
28946928 TTTATATATTACATAT-TACAAATTTA
1 TTTATATATT-CATATATACAAATTTA
28946954 TATATATTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (27 bp):
TTTATATATTCATATATACAAATTTAA
Found at i:28950531 original size:39 final size:39
Alignment explanation
Indices: 28950462--28950645 Score: 280
Period size: 39 Copynumber: 4.7 Consensus size: 39
28950452 ACAAAGCATG
* * * *
28950462 CGGGACTTTAAGCCTGGATATAATACCAGCAC-AAAGCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
28950502 CGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
28950542 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
28950581 CGGGACTTAGCCCGGATATAACACCAACACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
28950620 CAGGACTTAGCCCGGATATAACACCA
1 CGGGACTTAGCCCGGATATAACACCA
28950646 TTATAAAGTC
Statistics
Matches: 137, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
39 116 0.85
40 21 0.15
ACGTcount: A:0.30, C:0.29, G:0.22, T:0.18
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:28950751 original size:28 final size:28
Alignment explanation
Indices: 28950718--28950782 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
28950708 ATTTAATCAT
* *
28950718 TCAATATTTTGCATACTAAGTGTCATTC
1 TCAATATTTTGCACACTAAGTGCCATTC
* *
28950746 TCAATATCTTGCACATTAAGTGCCATTC
1 TCAATATTTTGCACACTAAGTGCCATTC
28950774 TCAATATTT
1 TCAATATTT
28950783 CGTACACTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.42
Consensus pattern (28 bp):
TCAATATTTTGCACACTAAGTGCCATTC
Found at i:28950799 original size:28 final size:28
Alignment explanation
Indices: 28950718--28950799 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
28950708 ATTTAATCAT
* * **
28950718 TCAATATTTTGCATACTAAGTGTCATTC
1 TCAATATCTTGCACACTAAGTACCATTC
* *
28950746 TCAATATCTTGCACATTAAGTGCCATTC
1 TCAATATCTTGCACACTAAGTACCATTC
* *
28950774 TCAATAT-TTCGTACACTGAGTACCAT
1 TCAATATCTT-GCACACTAAGTACCAT
28950800 ATTTGATTGC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
27 2 0.04
28 43 0.96
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (28 bp):
TCAATATCTTGCACACTAAGTACCATTC
Found at i:28952678 original size:18 final size:20
Alignment explanation
Indices: 28952651--28952690 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
28952641 AATTATACCC
28952651 CTATTATCATTTATCT-TTT
1 CTATTATCATTTATCTATTT
28952670 CTATT-TCATTTATCTATTT
1 CTATTATCATTTATCTATTT
28952689 CT
1 CT
28952691 CCAGTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.62
Consensus pattern (20 bp):
CTATTATCATTTATCTATTT
Found at i:28954831 original size:32 final size:32
Alignment explanation
Indices: 28954785--28954847 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
28954775 GATAGTAGAA
*
28954785 AAGATTATTTGGTTAAAAGCCAAGAAAAGACT
1 AAGAATATTTGGTTAAAAGCCAAGAAAAGACT
*
28954817 AAGAATATTTGGTTAAAAGCCAGGAAAAGAC
1 AAGAATATTTGGTTAAAAGCCAAGAAAAGAC
28954848 CTAAACTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.22
Consensus pattern (32 bp):
AAGAATATTTGGTTAAAAGCCAAGAAAAGACT
Found at i:28954953 original size:5 final size:5
Alignment explanation
Indices: 28954943--28954970 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28954933 ACCTATGTGA
28954943 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
28954971 GAACACACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:28963851 original size:14 final size:15
Alignment explanation
Indices: 28963832--28963890 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 15
28963822 TAGTTGGTAT
28963832 ATAAAAT-ATAAATA
1 ATAAAATAATAAATA
*
28963846 ATAAAAATATTTGAAATA
1 AT-AAAATA-AT-AAATA
*
28963864 ATAAAATGATAAA-A
1 ATAAAATAATAAATA
*
28963878 AGAAAATAATAAA
1 ATAAAATAATAAA
28963891 AAGAAATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
14 14 0.39
15 8 0.22
16 1 0.03
17 6 0.17
18 7 0.19
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.25
Consensus pattern (15 bp):
ATAAAATAATAAATA
Found at i:28963897 original size:13 final size:14
Alignment explanation
Indices: 28963866--28963896 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28963856 TTGAAATAAT
*
28963866 AAAATGATAAAAAG
1 AAAATAATAAAAAG
28963880 AAAATAATAAAAAG
1 AAAATAATAAAAAG
28963894 AAA
1 AAA
28963897 TTAAAACCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (14 bp):
AAAATAATAAAAAG
Found at i:28965352 original size:87 final size:88
Alignment explanation
Indices: 28965243--28965476 Score: 301
Period size: 87 Copynumber: 2.7 Consensus size: 88
28965233 TTCAGGGAGA
** *
28965243 TAAGGCTCACTGTCTTT-GATCTGCTCTGCTACTGTTTAGGGAGATAAGATCTGTAATTTCCAAC
1 TAAGGCTCACTGT-TTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAAC
28965307 CTATTACCCCACTACTTA-GGGGT
65 CTATTACCCCACTACTTAGGGGGT
* * * ** *
28965330 TAAGACTCACTGTTTTCGATCTGTTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTTTAGCC
1 TAAGGCTCACTGTTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAACC
* * *
28965395 TGTTACCCTACTGCTTAGGGGGT
66 TATTACCCCACTACTTAGGGGGT
* * * *
28965418 TAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAAATCTATAATTT
1 TAAGGCTCACTGTTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTT
28965477 TTAGCCTGTT
Statistics
Matches: 126, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
86 3 0.02
87 66 0.52
88 57 0.45
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (88 bp):
TAAGGCTCACTGTTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAACC
TATTACCCCACTACTTAGGGGGT
Found at i:28965452 original size:88 final size:87
Alignment explanation
Indices: 28965243--28965525 Score: 341
Period size: 88 Copynumber: 3.2 Consensus size: 87
28965233 TTCAGGGAGA
* * ** * ** *
28965243 TAAGGCTCACTGTCTTTGATCTGCTCTGCTACTGTTTAGGGAGATAAGATCTGTAATTTCCAACC
1 TAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCC
* * *
28965308 TATTACCCCACTACTTAGGGGT
66 TGTTACCCTACTGCTTAGGGGT
* * * * *
28965330 TAAGACTCACTGTTTTCGATCTGTTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTTTAGCC
1 TAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCC
28965395 TGTTACCCTACTGCTTAGGGGGT
66 TGTTACCCTACTGCTTA-GGGGT
* *
28965418 TAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAAATCTATAATTTTTAGCC
1 TAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCC
* * *
28965483 TGTTTCCTTACTGCTTAAGAGGT
66 TGTTACCCTACTGCTT-AGGGGT
* *
28965506 TAAGGCTTACCATCTTCGAT
1 TAAGGCTCACCGTCTTCGAT
28965526 AGGGAGATAA
Statistics
Matches: 168, Mismatches: 26, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
87 68 0.40
88 99 0.59
89 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.35
Consensus pattern (87 bp):
TAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCC
TGTTACCCTACTGCTTAGGGGT
Found at i:28965613 original size:43 final size:43
Alignment explanation
Indices: 28965560--28965878 Score: 133
Period size: 44 Copynumber: 7.3 Consensus size: 43
28965550 ACCTGTTACC
28965560 CTACTGCTTAGGGGTTAAGGCTCACCGTCTTCGAGCTGCTCCG
1 CTACTGCTTAGGGGTTAAGGCTCACCGTCTTCGAGCTGCTCCG
* * * * * * *
28965603 CTACTACTTAGGGAGATAA-GAT--CTGTAATTTCTAGCCTGTTACC-
1 CTACTGCTTAGGG-GTTAAGGCTCACCGT--CTTCGAG-CTGCT-CCG
* *
28965647 CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTTCG
1 CTACTGCTTA-GGGGTTAAGGCTCACCGTCTTCGAGCTGCTCCG
* * * * *
28965691 CTACTGCTTAGGGAGATT-A-GAT--CTGTAATTTCCAGCCTGTTACC-
1 CTACTGCTTAGGG-G-TTAAGGCTCACCGT--CTTCGAG-CTGCT-CCG
* *
28965735 CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCG
1 CTACTGCTTA-GGGGTTAAGGCTCACCGTCTTCGAGCTGCTCCG
* * * * * * **
28965779 CTACTGTTTAGGGAGATAA-GAT--CTGTAATTTCCAGCCTATTACC-
1 CTACTGCTTAGGG-GTTAAGGCTCACCGT--CTTCGAG-CTGCT-CCG
** *
28965823 CTACTGCTTAGGGGTTAAGGCTCACCGTCTTTTATCTGCTCCG
1 CTACTGCTTAGGGGTTAAGGCTCACCGTCTTCGAGCTGCTCCG
*
28965866 CTACTACTTAGGG
1 CTACTGCTTAGGG
28965879 AGATTAGATC
Statistics
Matches: 194, Mismatches: 51, Indels: 62
0.63 0.17 0.20
Matches are distributed among these distances:
41 9 0.05
42 2 0.01
43 60 0.31
44 90 0.46
45 24 0.12
46 3 0.02
47 6 0.03
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (43 bp):
CTACTGCTTAGGGGTTAAGGCTCACCGTCTTCGAGCTGCTCCG
Found at i:28965888 original size:87 final size:88
Alignment explanation
Indices: 28965525--28966271 Score: 992
Period size: 88 Copynumber: 8.7 Consensus size: 88
28965515 CCATCTTCGA
*
28965525 TAGGGAGATAAGATCTATAATTTTCA-CCTGTTACCCTACTGCTTA-GGGGTTAAGGCTCACCGT
1 TAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
* * *
28965588 CTTCGAGCTGCTCCGCTACTACT
66 CTTCGATCTGCTCCACTACTGCT
28965611 TAGGGAGATAAGATCTGTAA-TTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCG
1 TAGGGAGATAAGATCTGTAATTTTC-AGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCG
* *
28965675 TCTTCGATCTGCTTCGCTACTGCT
65 TCTTCGATCTGCTCCACTACTGCT
* *
28965699 TAGGGAGATTAGATCTGTAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
1 TAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
* * *
28965764 CTTTGATCTGCTCCGCTACTGTT
66 CTTCGATCTGCTCCACTACTGCT
* *
28965787 TAGGGAGATAAGATCTGTAATTTCCAGCCTATTACCCTACTGCTTA-GGGGTTAAGGCTCACCGT
1 TAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
** * *
28965851 CTTTTATCTGCTCCGCTACTACT
66 CTTCGATCTGCTCCACTACTGCT
* * * *
28965874 TAGGGAGATTAGATCTATAATTTTCAGCCTGTTACCCTACTGCTTAGGAGGTTAAAGCTC-CCGT
1 TAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
**
28965938 CTTCGATCTGCTCCACTACTTTT
66 CTTCGATCTGCTCCACTACTGCT
* * * * ** *
28965961 TA-GGAG---AGATCTGTATTTTTCAACCTATTACCCTACTACTTA-GGGGTTAAGGCTTGCTGT
1 TAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
28966021 CTTCGATCTGCTCCACTACTGCT
66 CTTCGATCTGCTCCACTACTGCT
* *
28966044 TAGGAAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACTGT
1 TAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
*
28966109 CTTCGATCTGCTCCACTACTGTT
66 CTTCGATCTGCTCCACTACTGCT
* * * *
28966132 TA-GGAG---AGATCTGTATTTTTGAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACTGT
1 TAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
*
28966193 CTTCGATCTGCTCCACTACTGTT
66 CTTCGATCTGCTCCACTACTGCT
*
28966216 TA-GG-G--AAGATCTGT-ATTTTCTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTC
1 TAGGGAGATAAGATCTGTAATTTTC-AGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTC
28966272 GTGGATTCAC
Statistics
Matches: 596, Mismatches: 52, Indels: 28
0.88 0.08 0.04
Matches are distributed among these distances:
82 10 0.02
83 62 0.10
84 123 0.21
85 4 0.01
86 24 0.04
87 158 0.27
88 212 0.36
89 3 0.01
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (88 bp):
TAGGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGT
CTTCGATCTGCTCCACTACTGCT
Found at i:28966128 original size:44 final size:44
Alignment explanation
Indices: 28965993--28966220 Score: 140
Period size: 44 Copynumber: 5.3 Consensus size: 44
28965983 ACCTATTACC
* *
28965993 CTACTACTTA-GGGGTTAAGGCTTGCTGTCTTCGATCTGCTCCA
1 CTACTGCTTAGGGGGTTAAGGCTTACTGTCTTCGATCTGCTCCA
** * * * * *
28966036 CTACTGCTTAGGAAGATAAGATCTGTAAT-T-TTC-AGCCTGTTACC-
1 CTACTGCTTAGGGGGTTAAG-GCT-TACTGTCTTCGA-TCTGCT-CCA
*
28966080 CTACTGCTTAGGGGGTTAAGGCTCACTGTCTTCGATCTGCTCCA
1 CTACTGCTTAGGGGGTTAAGGCTTACTGTCTTCGATCTGCTCCA
* * * * * *
28966124 CTACTGTTTA-GGAG---AGATCTGTA-T-T-TTTGAGCCTGTTACC-
1 CTACTGCTTAGGGGGTTAAG-GCT-TACTGTCTTCGA-TCTGCT-CCA
28966164 CTACTGCTTAGGGGGTTAAGGCTTACTGTCTTCGATCTGCTCCA
1 CTACTGCTTAGGGGGTTAAGGCTTACTGTCTTCGATCTGCTCCA
*
28966208 CTACTGTTTAGGG
1 CTACTGCTTAGGG
28966221 AAGATCTGTA
Statistics
Matches: 133, Mismatches: 31, Indels: 41
0.65 0.15 0.20
Matches are distributed among these distances:
39 4 0.03
40 16 0.12
41 8 0.06
42 5 0.04
43 23 0.17
44 65 0.49
45 10 0.08
46 2 0.02
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (44 bp):
CTACTGCTTAGGGGGTTAAGGCTTACTGTCTTCGATCTGCTCCA
Found at i:28966772 original size:128 final size:127
Alignment explanation
Indices: 28966629--28966882 Score: 427
Period size: 128 Copynumber: 2.0 Consensus size: 127
28966619 AAGTGTGTGC
* * * * *
28966629 ACAACTCGAGTTGGATTTTAGGATTCACTCGTTCCAAAGGAATAAAATACCACATCCATCATGTT
1 ACAACTCAAGTTGGATATTAAGATTCACTCGTTCCAAAGGAATAAAATACCACATCCAGCACGTT
*
28966694 AGGACACGATATTTTAAGCCTCAAAAAAACTGAGATCACCTCATGATTTCCAAAACATGCGAA
66 AAGACACGATATTTTAAGCCTC-AAAAAACTGAGATCACCTCATGATTTCCAAAACATGCGAA
28966757 ACAACTCAAGTTGGATATTAAGATTCACTCGTTCCAAAGGAATAAAATACCACATCCAGCACGTT
1 ACAACTCAAGTTGGATATTAAGATTCACTCGTTCCAAAGGAATAAAATACCACATCCAGCACGTT
* *
28966822 AAGACACGATATTTTAAGCCTCCAAAAATTGAGATCACCTCATGATTTCCAAAACATGCGA
66 AAGACACGATATTTTAAGCCTCAAAAAACTGAGATCACCTCATGATTTCCAAAACATGCGA
28966883 CGAAAATTTT
Statistics
Matches: 118, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
127 37 0.31
128 81 0.69
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (127 bp):
ACAACTCAAGTTGGATATTAAGATTCACTCGTTCCAAAGGAATAAAATACCACATCCAGCACGTT
AAGACACGATATTTTAAGCCTCAAAAAACTGAGATCACCTCATGATTTCCAAAACATGCGAA
Found at i:28969492 original size:177 final size:177
Alignment explanation
Indices: 28969115--28969920 Score: 1225
Period size: 177 Copynumber: 4.5 Consensus size: 177
28969105 AGACAAAGCA
** *
28969115 GGTGGCTAAAATCTGCTCCATAATCGATACATGGAGATAAGACTCGCCATCTTCGATCTGCTCCA
1 GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCA
* * * *
28969180 TAGCCGATACATGGCGATAAGATCTGTAATTTTTAGTCTGCTTCCTTGCTGCCTTAGGAAGATAA
66 TAGCCGATACATGGAGATAAGATCTGTAA-TTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAA
* *
28969245 GACTTGTACCTTTAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
130 GACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
* * *
28969293 GGTGGCTAAAATCTGCTCCATAGTCGATACATGGAGATAAGATTCGCCATCTTCAATCTGTTCCA
1 GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCA
* *
28969358 TAGCCTATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCATTGCTACCTCAGGAAGATAAG
66 TAGCCGATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAG
* * * *
28969423 ACTTGTATCTTTAACCTTCTATTTTGCTACCTCAGAGAGATAAGGCT
131 ACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
* * * * * *
28969470 GCTGGCTAAAATCTACTCCATAGCCAATACATGAAGATAAGATTCGCCATCTTCAACCTGCTCCA
1 GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCA
* * * ** *
28969535 TAGCCGATACGTGGAGATAAGATCTGCAATTTCAATCTGCTTCCTTATTACCTCAGGAAGGTAAG
66 TAGCCGATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAG
* *
28969600 ACTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAAGCT
131 ACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
* * *
28969647 GGTGGCTAAAATCTACTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTTGATCTACTCCA
1 GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCA
* *
28969712 TTGCCGATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAAG
66 TAGCCGATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAG
28969777 ACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
131 ACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
* * * * *
28969824 AGTGCCTAAAATCTGCTCCATAGCCGATATATGGAGATAAGATTCACCATCTTCGATCTGCTCTA
1 GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCA
28969889 TAGCCGATACATGGAGATAAGATCTGTAATTT
66 TAGCCGATACATGGAGATAAGATCTGTAATTT
28969921 TATCGACATC
Statistics
Matches: 567, Mismatches: 61, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
177 479 0.84
178 88 0.16
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (177 bp):
GGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCA
TAGCCGATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAG
ACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCT
Found at i:28974315 original size:21 final size:21
Alignment explanation
Indices: 28974290--28974333 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
28974280 GAAATGCAAG
* *
28974290 AAAAGAAGATTTGCTCAAGAT
1 AAAAGAAGATATGCTCAAAAT
*
28974311 AAAAGAATATATGCTCAAAAT
1 AAAAGAAGATATGCTCAAAAT
28974332 AA
1 AA
28974334 GACATAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.09, G:0.14, T:0.23
Consensus pattern (21 bp):
AAAAGAAGATATGCTCAAAAT
Found at i:28982541 original size:20 final size:20
Alignment explanation
Indices: 28982516--28982568 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
28982506 CCTTCCACAA
*
28982516 TTTTTTTTTTGTC-TTTTTTG
1 TTTTTTTTTT-TCACTTTTTG
28982536 TTTTTTTTTTTCACTTTTTG
1 TTTTTTTTTTTCACTTTTTG
28982556 TTTCTTTCTTTTT
1 TTT-TTT-TTTTT
28982569 GGCTGCCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 2 0.07
20 19 0.66
21 3 0.10
22 5 0.17
ACGTcount: A:0.02, C:0.09, G:0.06, T:0.83
Consensus pattern (20 bp):
TTTTTTTTTTTCACTTTTTG
Done.