Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008426.1 Hibiscus syriacus cultivar Beakdansim tig00111210_pilon, whole genome shotgun sequence
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: 4445546
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 18
Found at i:2729125 original size:29 final size:29
Alignment explanation
Indices: 2729076--2729132 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2729066 ACTACTCTCT
*
2729076 GGTGAAGGCTTCAGATAGTTTGCTTCACC
1 GGTGAAGGATTCAGATAGTTTGCTTCACC
* *
2729105 GGTGAAGGATT-AGGATGGTTTTCTTCAC
1 GGTGAAGGATTCA-GATAGTTTGCTTCAC
2729133 TACTTTTCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (29 bp):
GGTGAAGGATTCAGATAGTTTGCTTCACC
Found at i:2729147 original size:65 final size:65
Alignment explanation
Indices: 2729038--2729168 Score: 160
Period size: 65 Copynumber: 2.0 Consensus size: 65
2729028 TCACTATTCT
* *
2729038 CCGGTGAAGACTTAGGATGATTTGCTTCACTACTCTCTGGTGAAGGCTTCA-GATAGTTTGCTTC
1 CCGGTGAAGACTTAGGATGATTTGCTTCACTACTCTCTGATGAAGGCCT-AGGATAGTTTGCTTC
2729102 A
65 A
* * * *
2729103 CCGGTGAAGGA-TTAGGATGGTTTTCTTCACTACT-TTTCGATGAAGGCCTAGGATGGTTTGCTT
1 CCGGTGAA-GACTTAGGATGATTTGCTTCACTACTCTCT-GATGAAGGCCTAGGATAGTTTGCTT
2729166 CA
64 CA
2729168 C
1 C
2729169 TACTCTCCAG
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
64 3 0.05
65 52 0.91
66 2 0.04
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (65 bp):
CCGGTGAAGACTTAGGATGATTTGCTTCACTACTCTCTGATGAAGGCCTAGGATAGTTTGCTTCA
Found at i:2729172 original size:173 final size:171
Alignment explanation
Indices: 2728931--2729262 Score: 468
Period size: 173 Copynumber: 1.9 Consensus size: 171
2728921 CACTACTCTT
* * *
2728931 CGGTGAAGGCTTAAGATGGATTGCTTCACTCCTCTTCAGTGAAGGCTTAAGATGGTTTGCTTCAC
1 CGGTGAAGGATTAAGATGGATTGCTTCACTACTCTTCAGTGAAGGCCTAAGATGGTTTGCTTCAC
*** * * *
2728996 TACTCTTTGGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCCGGTGAAGACTTAGGATGATTT
66 TACTCTCCAGTGAAGGCATCAGATGGTTTGCTTCACTATTCTCCGATGAAGACTTAGGATG--GT
*
2729061 GCTTCACTACTCTCTGGTGAAGGCTTCAGATAGTTTGCTTCAC
129 GCTTCACTACTCTCTGGTGAAGGCTTAAGATAGTTTGCTTCAC
* * * * *
2729104 CGGTGAAGGATTAGGATGGTTTTCTTCACTACTTTTC-GATGAAGGCCTAGGATGGTTTGCTTCA
1 CGGTGAAGGATTAAGATGGATTGCTTCACTACTCTTCAG-TGAAGGCCTAAGATGGTTTGCTTCA
*
2729168 CTACTCTCCAGTGAAGGCATCAGATGGTTTGCTTCACTATTCTCCGATGAAGGCTTAGGATGGTG
65 CTACTCTCCAGTGAAGGCATCAGATGGTTTGCTTCACTATTCTCCGATGAAGACTTAGGATGGTG
* *
2729233 CTTCACTCCTCTTTGGTGAAGGCTTAAGAT
130 CTTCACTACTCTCTGGTGAAGGCTTAAGAT
2729263 TGATTACTTC
Statistics
Matches: 140, Mismatches: 18, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
171 29 0.21
172 1 0.01
173 110 0.79
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (171 bp):
CGGTGAAGGATTAAGATGGATTGCTTCACTACTCTTCAGTGAAGGCCTAAGATGGTTTGCTTCAC
TACTCTCCAGTGAAGGCATCAGATGGTTTGCTTCACTATTCTCCGATGAAGACTTAGGATGGTGC
TTCACTACTCTCTGGTGAAGGCTTAAGATAGTTTGCTTCAC
Found at i:2730506 original size:125 final size:125
Alignment explanation
Indices: 2730284--2730509 Score: 321
Period size: 125 Copynumber: 1.8 Consensus size: 125
2730274 CACAATATTA
* * * * *
2730284 TCTCATACTGGTACGGACCTTCAAAATGCCCCAACATCTCAGATTGTAAGGCTCACTCTCAATGC
1 TCTCATACTGGTACGGACCTTCAAAATACCCCAACACCTCAAATTGTAAGGCTAACTCTCAATAC
2730349 CTTCTTGGTCTAAATCTTGTCATCTCAACATGATGTGGGTTCAGTCATGCCCCATCAGTG
66 CTTCTTGGTCTAAATCTTGTCATCTCAACATGATGTGGGTTCAGTCATGCCCCATCAGTG
* * * *
2730409 TCTCATACTGGTACGGGCCTTCAAAATACCCCATCACCTCAAATTGTAAGGCTAATTCTTC-TTA
1 TCTCATACTGGTACGGACCTTCAAAATACCCCAACACCTCAAATTGTAAGGCTAACTC-TCAATA
* *
2730473 CC-TCATTGGTCTAAATCTTGTTATTTCAACATGATGT
65 CCTTC-TTGGTCTAAATCTTGTCATCTCAACATGATGT
2730510 AGGCTTAATC
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
124 2 0.02
125 84 0.95
126 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (125 bp):
TCTCATACTGGTACGGACCTTCAAAATACCCCAACACCTCAAATTGTAAGGCTAACTCTCAATAC
CTTCTTGGTCTAAATCTTGTCATCTCAACATGATGTGGGTTCAGTCATGCCCCATCAGTG
Found at i:2734487 original size:393 final size:393
Alignment explanation
Indices: 2733762--2734547 Score: 1554
Period size: 393 Copynumber: 2.0 Consensus size: 393
2733752 TTTCTAATTA
2733762 ATGCATGTAAAAATGCTTAAATAAATACATGCAATGTAAATGCAAATGCTAAATGCAAGTACAAA
1 ATGCATGTAAAAATGCTTAAATAAATACATGCAATGTAAATGCAAATGCTAAATGCAAGTACAAA
2733827 AGGTGTCATTTTAGAGTAACCATCTTAAAACAACTTTCATTGAACATAAAGGTTTTGGTACATCA
66 AGGTGTCATTTTAGAGTAACCATCTTAAAACAACTTTCATTGAACATAAAGGTTTTGGTACATCA
2733892 AACAAACTTTTATAGATAACGGACAGCTTTCACCCCTAGCTTTTCTATCTCCTTCAAAAGCTAAA
131 AACAAACTTTTATAGATAACGGACAGCTTTCACCCCTAGCTTTTCTATCTCCTTCAAAAGCTAAA
*
2733957 GTAACTTTCACTCATGCTCGGAGATTGAGTTGTCTATTTGCTTCAATTCCCTTGCAAATCCCGCT
196 GTAACTTTCACTCATGCTCGGAGATTGAGTTGTCTATTTGCCTCAATTCCCTTGCAAATCCCGCT
2734022 AAATCAACTAATTTGTGAGCCAAAATGCTTGCTTAGGTCATAGCTTCTTCCATGACGTCGTCCCT
261 AAATCAACTAATTTGTGAGCCAAAATGCTTGCTTAGGTCATAGCTTCTTCCATGACGTCGTCCCT
2734087 TTTCTCTATCTTAAGCACCAATTCTTGGAGATGCAGACACTGCATCTGATTTTTCCTTGTAAGAA
326 TTTCTCTATCTTAAGCACCAATTCTTGGAGATGCAGACACTGCATCTGATTTTTCCTTGTAAGAA
2734152 AGT
391 AGT
2734155 ATGCATGTAAAAATGCTTAAATAAATACATGCAATGTAAATGCAAATGCTAAATGCAAGTACAAA
1 ATGCATGTAAAAATGCTTAAATAAATACATGCAATGTAAATGCAAATGCTAAATGCAAGTACAAA
2734220 AGGTGTCATTTTAGAGTAACCATCTTAAAACAACTTTCATTGAACATAAAGGTTTTGGTACATCA
66 AGGTGTCATTTTAGAGTAACCATCTTAAAACAACTTTCATTGAACATAAAGGTTTTGGTACATCA
2734285 AACAAACTTTTATAGATAACGGACAGCTTTCACCCCTAGCTTTTCTATCTCCTTCAAAAGCTAAA
131 AACAAACTTTTATAGATAACGGACAGCTTTCACCCCTAGCTTTTCTATCTCCTTCAAAAGCTAAA
*
2734350 GTAACTTTCACTCATGCTCGGGGATTGAGTTGTCTATTTGCCTCAATTCCCTTGCAAATCCCGCT
196 GTAACTTTCACTCATGCTCGGAGATTGAGTTGTCTATTTGCCTCAATTCCCTTGCAAATCCCGCT
2734415 AAATCAACTAATTTGTGAGCCAAAATGCTTGCTTAGGTCATAGCTTCTTCCATGACGTCGTCCCT
261 AAATCAACTAATTTGTGAGCCAAAATGCTTGCTTAGGTCATAGCTTCTTCCATGACGTCGTCCCT
2734480 TTTCTCTATCTTAAGCACCAATTCTTGGAGATGCAGACACTGCATCTGATTTTTCCTTGTAAGAA
326 TTTCTCTATCTTAAGCACCAATTCTTGGAGATGCAGACACTGCATCTGATTTTTCCTTGTAAGAA
2734545 AGT
391 AGT
2734548 CGTTGTGGTT
Statistics
Matches: 391, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
393 391 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (393 bp):
ATGCATGTAAAAATGCTTAAATAAATACATGCAATGTAAATGCAAATGCTAAATGCAAGTACAAA
AGGTGTCATTTTAGAGTAACCATCTTAAAACAACTTTCATTGAACATAAAGGTTTTGGTACATCA
AACAAACTTTTATAGATAACGGACAGCTTTCACCCCTAGCTTTTCTATCTCCTTCAAAAGCTAAA
GTAACTTTCACTCATGCTCGGAGATTGAGTTGTCTATTTGCCTCAATTCCCTTGCAAATCCCGCT
AAATCAACTAATTTGTGAGCCAAAATGCTTGCTTAGGTCATAGCTTCTTCCATGACGTCGTCCCT
TTTCTCTATCTTAAGCACCAATTCTTGGAGATGCAGACACTGCATCTGATTTTTCCTTGTAAGAA
AGT
Found at i:2736413 original size:56 final size:55
Alignment explanation
Indices: 2736349--2736492 Score: 166
Period size: 56 Copynumber: 2.6 Consensus size: 55
2736339 TAACTTCAAA
* * *
2736349 CTTCATTCATCGGATGTCTTTCTTCATGGATCGA-TCTTCAATCAATTTCAGATTTT
1 CTTCATTCATCGGATGTCTTTCTTCATGAATC-ATTCTTCAATCAAGTTCA-AATTT
* * *
2736405 CTTCATTCATCAGATGT-TCATCTTCATGAATCATTCTTCAATCAGGTTCAAATTT
1 CTTCATTCATCGGATGTCT-TTCTTCATGAATCATTCTTCAATCAAGTTCAAATTT
* * *
2736460 CATCATTCATAGGATGTCCTTCTTCATGAATCA
1 CTTCATTCATCGGATGTCTTTCTTCATGAATCA
2736493 CTTGAATGTC
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
55 33 0.45
56 41 0.55
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (55 bp):
CTTCATTCATCGGATGTCTTTCTTCATGAATCATTCTTCAATCAAGTTCAAATTT
Found at i:2740168 original size:15 final size:16
Alignment explanation
Indices: 2740148--2740183 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2740138 TAAAAAATTA
2740148 ATAATAATAAT-TATT
1 ATAATAATAATATATT
2740163 ATAATAATAATATATT
1 ATAATAATAATATATT
2740179 -TAATA
1 ATAATA
2740184 TTTATAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATAATAATATATT
Found at i:2741134 original size:24 final size:25
Alignment explanation
Indices: 2741091--2741139 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
2741081 TGGTTGTTAA
*
2741091 ATATGATTTTTACCACGAAT-ATAT
1 ATATGATATTTACCACGAATGATAT
* *
2741115 ATATGATATTTATCATGAATGATAT
1 ATATGATATTTACCACGAATGATAT
2741140 TTTGGGTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (25 bp):
ATATGATATTTACCACGAATGATAT
Found at i:2748708 original size:17 final size:18
Alignment explanation
Indices: 2748688--2748721 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2748678 ATAAAGAGCT
2748688 AGTTTAAAT-AATGAACC
1 AGTTTAAATGAATGAACC
2748705 AGTTTAAATGAATGAAC
1 AGTTTAAATGAATGAAC
2748722 TATTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (18 bp):
AGTTTAAATGAATGAACC
Found at i:2749058 original size:23 final size:23
Alignment explanation
Indices: 2749031--2749084 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
2749021 CCCATATTAA
2749031 GCTCGAATAAACTTCTAGAAGCT
1 GCTCGAATAAACTTCTAGAAGCT
2749054 GCTCGAATAAACTTCTAGAAGCT
1 GCTCGAATAAACTTCTAGAAGCT
*
2749077 TCTCGAAT
1 GCTCGAAT
2749085 GTAAACAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (23 bp):
GCTCGAATAAACTTCTAGAAGCT
Found at i:2749422 original size:22 final size:23
Alignment explanation
Indices: 2749396--2749442 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2749386 TGATTGTAAC
*
2749396 ATATGATGTTTATCATGAAT-AT
1 ATATGATATTTATCATGAATGAT
*
2749418 ATATGATATTTATTATGAATGAT
1 ATATGATATTTATCATGAATGAT
2749441 AT
1 AT
2749443 TTTGGGTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (23 bp):
ATATGATATTTATCATGAATGAT
Found at i:2749738 original size:61 final size:61
Alignment explanation
Indices: 2749612--2749743 Score: 147
Period size: 61 Copynumber: 2.2 Consensus size: 61
2749602 CAAGGACACT
* * * **
2749612 TAGTGCACGTGGTGGGCACAACCTTATGTGTCACACCCAAATCAACACTAGAGTGTAAACC
1 TAGTGCAGGTAGTGGGCACAACCATATGTGTCACACCCAAATCAACACTAGAGCATAAACC
* * * * * * * *
2749673 TAGTGTAGGTAGTGGGCACGACCATATGTGTCATATCCGAATCAGCACTAGAGCATAAGCT
1 TAGTGCAGGTAGTGGGCACAACCATATGTGTCACACCCAAATCAACACTAGAGCATAAACC
2749734 TAGTGCAGGT
1 TAGTGCAGGT
2749744 TTACCACTAC
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (61 bp):
TAGTGCAGGTAGTGGGCACAACCATATGTGTCACACCCAAATCAACACTAGAGCATAAACC
Found at i:2751480 original size:69 final size:69
Alignment explanation
Indices: 2751369--2751507 Score: 242
Period size: 69 Copynumber: 2.0 Consensus size: 69
2751359 CAAAGATGAG
2751369 AATTAAAATGAAAATACATGAGATAATATGATTTTAAAGGCAGCGAACAATCAACCTTGCATGTA
1 AATTAAAATGAAAATACATGAGATAATATGATTTTAAAGGCAGCGAACAATCAACCTTGCATGTA
2751434 GCTT
66 GCTT
* * **
2751438 AATTAAAATGAAAATACATGAGATAATATTATTTTAAAGGCAGTGAACAATTGACCTTGCATGTA
1 AATTAAAATGAAAATACATGAGATAATATGATTTTAAAGGCAGCGAACAATCAACCTTGCATGTA
2751503 GCTT
66 GCTT
2751507 A
1 A
2751508 CTTTTAGACT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (69 bp):
AATTAAAATGAAAATACATGAGATAATATGATTTTAAAGGCAGCGAACAATCAACCTTGCATGTA
GCTT
Found at i:2757303 original size:16 final size:17
Alignment explanation
Indices: 2757282--2757315 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2757272 TTTCATTATT
*
2757282 ATTTAATATA-AAAATA
1 ATTTAAAATATAAAATA
2757298 ATTTAAAATATAAAATA
1 ATTTAAAATATAAAATA
2757315 A
1 A
2757316 AAATAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAATATAAAATA
Found at i:2758730 original size:32 final size:32
Alignment explanation
Indices: 2758693--2758764 Score: 144
Period size: 32 Copynumber: 2.2 Consensus size: 32
2758683 GCTGCAGCCC
2758693 TTAATTTATTAATAATGTTATAGATAAATTAT
1 TTAATTTATTAATAATGTTATAGATAAATTAT
2758725 TTAATTTATTAATAATGTTATAGATAAATTAT
1 TTAATTTATTAATAATGTTATAGATAAATTAT
2758757 TTAATTTA
1 TTAATTTA
2758765 AAAAACTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (32 bp):
TTAATTTATTAATAATGTTATAGATAAATTAT
Found at i:2759443 original size:16 final size:16
Alignment explanation
Indices: 2759419--2759453 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2759409 GAAACCCATT
* *
2759419 AATATTTTTAAACTCA
1 AATAGTTTTAAACCCA
2759435 AATAGTTTTAAACCCA
1 AATAGTTTTAAACCCA
2759451 AAT
1 AAT
2759454 GAAAATAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (16 bp):
AATAGTTTTAAACCCA
Found at i:2759609 original size:24 final size:24
Alignment explanation
Indices: 2759550--2759613 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
2759540 TTTATTTTTG
* *
2759550 TTCGTTTATATTCACTCACGTTCT
1 TTCGTTTATGTTCGCTCACGTTCT
*
2759574 TTCGTTTATGTTCGCTCATGTTCT
1 TTCGTTTATGTTCGCTCACGTTCT
*
2759598 TTCGTTTGTGTTCGCT
1 TTCGTTTATGTTCGCT
2759614 TACCATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.09, C:0.22, G:0.16, T:0.53
Consensus pattern (24 bp):
TTCGTTTATGTTCGCTCACGTTCT
Found at i:2759654 original size:31 final size:30
Alignment explanation
Indices: 2759619--2759679 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
2759609 TCGCTTACCA
*
2759619 TTTTAATGAATGAAAAAGAACAAGATAATTT
1 TTTTAATGAACGAAAAAGAACAAGA-AATTT
* *
2759650 TTTTAATGAACGAACACGAACAAGAAATTT
1 TTTTAATGAACGAAAAAGAACAAGAAATTT
2759680 CATTCTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (30 bp):
TTTTAATGAACGAAAAAGAACAAGAAATTT
Found at i:2759983 original size:13 final size:13
Alignment explanation
Indices: 2759965--2759989 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2759955 AGAAATGGGT
2759965 ATTGTTATCAGAC
1 ATTGTTATCAGAC
2759978 ATTGTTATCAGA
1 ATTGTTATCAGA
2759990 TAGGCAAGAA
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:0.12, G:0.16, T:0.40
Consensus pattern (13 bp):
ATTGTTATCAGAC
Found at i:2762192 original size:36 final size:36
Alignment explanation
Indices: 2762152--2762221 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
2762142 ATCCCTCAAA
*
2762152 CCCATCCAGCCTAGTATAGTGAAGCAGTGATCAATC
1 CCCATCCAGCCTAGTATAGTGAAGCAATGATCAATC
*
2762188 CCCATCCAGCCTAGTATAGTGAATCAATGATCAA
1 CCCATCCAGCCTAGTATAGTGAAGCAATGATCAA
2762222 CGCAAATTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (36 bp):
CCCATCCAGCCTAGTATAGTGAAGCAATGATCAATC
Found at i:2764044 original size:27 final size:27
Alignment explanation
Indices: 2763992--2764042 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
2763982 AAAACGGTTT
*
2763992 GGTTCGGTTTTAAAAGGTTTGATTTTC
1 GGTTCGGTTTTAAAAGGTTTCATTTTC
2764019 GGTTCGG-TTT-AAAGGTTTCATTTT
1 GGTTCGGTTTTAAAAGGTTTCATTTT
2764043 TTTGATTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.57
26 3 0.13
27 7 0.30
ACGTcount: A:0.18, C:0.08, G:0.25, T:0.49
Consensus pattern (27 bp):
GGTTCGGTTTTAAAAGGTTTCATTTTC
Found at i:2767151 original size:57 final size:58
Alignment explanation
Indices: 2767079--2767196 Score: 195
Period size: 57 Copynumber: 2.1 Consensus size: 58
2767069 TCATTCTTTG
* *
2767079 TTTACTTTAATTTTCATTCACATATTATAAGTACATCAAATGAATGT-AAAGAATACA
1 TTTACTTTAATTTTCATTCACAAATTATAAGTACATCAAATGAATATAAAAGAATACA
2767136 TTTAC-TTAAGTTTTCATTCACAAATTATAAGTACATCAAATGAATATAAAAGAATACA
1 TTTACTTTAA-TTTTCATTCACAAATTATAAGTACATCAAATGAATATAAAAGAATACA
2767194 TTT
1 TTT
2767197 TAAATGAAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
56 4 0.07
57 40 0.70
58 13 0.23
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (58 bp):
TTTACTTTAATTTTCATTCACAAATTATAAGTACATCAAATGAATATAAAAGAATACA
Found at i:2775928 original size:33 final size:33
Alignment explanation
Indices: 2775877--2775940 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
2775867 CTCTAGGAGC
* *
2775877 GGTCATAAAACTCTGTGACGGTGGTGGCGGCAG
1 GGTCATAAAACTCAGTGACGGTGGCGGCGGCAG
*
2775910 GGTCATAAAAC-CAAGTGACTGTGGCGGCGGC
1 GGTCATAAAACTC-AGTGACGGTGGCGGCGGC
2775941 GACATTGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 1 0.04
33 26 0.96
ACGTcount: A:0.23, C:0.20, G:0.38, T:0.19
Consensus pattern (33 bp):
GGTCATAAAACTCAGTGACGGTGGCGGCGGCAG
Found at i:2785346 original size:49 final size:49
Alignment explanation
Indices: 2785273--2785445 Score: 224
Period size: 49 Copynumber: 3.6 Consensus size: 49
2785263 GAATACCATA
* *
2785273 AGTGGCACCTTTTATGCTGAAATGCACCGTTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAAATTTCATT
* * * * *
2785322 CGTGGCACGTTTTATGCCGAAATGCATCGTTATGAATTTAAATTTTATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAAATTTCATT
* * *
2785371 AGTGGCACCTTTTATGCCAAAATGCACCATTATGCATTT-ATTTTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAAATTTCATT
* *
2785419 AGCGACA-CTTTTATGCCGAAATGCACC
1 AGTGGCACCTTTTATGCCGAAATGCACC
2785446 TTTTATGCCG
Statistics
Matches: 106, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
47 19 0.18
48 12 0.11
49 75 0.71
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (49 bp):
AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAAATTTCATT
Found at i:2785450 original size:19 final size:19
Alignment explanation
Indices: 2785426--2785464 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2785416 ATTAGCGACA
2785426 CTTTTATGCCGAAATGCAC
1 CTTTTATGCCGAAATGCAC
2785445 CTTTTATGCCGAAATGCAC
1 CTTTTATGCCGAAATGCAC
2785464 C
1 C
2785465 ATTCTGCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (19 bp):
CTTTTATGCCGAAATGCAC
Found at i:2792155 original size:49 final size:48
Alignment explanation
Indices: 2792100--2792242 Score: 171
Period size: 49 Copynumber: 2.9 Consensus size: 48
2792090 ACCATGAGTG
* *
2792100 GCACCTTTTATCCCGAAATGCACTGTTATTCATTTAACTTTCATTAGTA
1 GCACCTTTTATGCCGAAATACACT-TTATTCATTTAACTTTCATTAGTA
* *
2792149 GCACCTTTTATGCCGAAATTCACCTTTATGT-ATTTAACTTTCATTAGTT
1 GCACCTTTTATGCCGAAATACA-CTTTAT-TCATTTAACTTTCATTAGTA
* * * *
2792198 GCACCTTTTATGTCGAAATACACCATTATGCATTTAATTTTCATT
1 GCACCTTTTATGCCGAAATACA-CTTTATTCATTTAACTTTCATT
2792243 CATTCATTCA
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
49 80 0.96
50 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.43
Consensus pattern (48 bp):
GCACCTTTTATGCCGAAATACACTTTATTCATTTAACTTTCATTAGTA
Found at i:2792246 original size:4 final size:4
Alignment explanation
Indices: 2792237--2792262 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2792227 GCATTTAATT
2792237 TTCA TTCA TTCA TTCA TTCA TTCA TT
1 TTCA TTCA TTCA TTCA TTCA TTCA TT
2792263 AGAGGAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (4 bp):
TTCA
Found at i:2797200 original size:22 final size:22
Alignment explanation
Indices: 2797126--2797202 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
2797116 CAGAAGTGTC
* *
2797126 TTAGCACTAATACTAAAGTGCC
1 TTAGCACTGATACTAAAGTGCA
* *
2797148 TCT-GCACTTATA-TAGAAGTGTA
1 T-TAGCACTGATACTA-AAGTGCA
2797170 TTCA-CACTGATACTAAAGTGCA
1 TT-AGCACTGATACTAAAGTGCA
2797192 TTAGCACTGAT
1 TTAGCACTGAT
2797203 GGATAATCTG
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
21 4 0.09
22 37 0.84
23 3 0.07
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (22 bp):
TTAGCACTGATACTAAAGTGCA
Found at i:2807889 original size:22 final size:22
Alignment explanation
Indices: 2807831--2807890 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
2807821 AAGTACCTTG
* *
2807831 CACTAATACTAAAGTTCCTCAT
1 CACTGATACTAAAGTGCCTCAT
*
2807853 CACTGATAC-AGAAGTGCATTCAT
1 CACTGATACTA-AAGTGC-CTCAT
2807876 -ACTGATACTAAAGTG
1 CACTGATACTAAAGTG
2807891 ACTTAGCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 1 0.03
22 26 0.81
23 5 0.16
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (22 bp):
CACTGATACTAAAGTGCCTCAT
Found at i:2810489 original size:13 final size:13
Alignment explanation
Indices: 2810471--2810496 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2810461 AAAATTCATA
2810471 TTTTTGAATGAAT
1 TTTTTGAATGAAT
2810484 TTTTTGAATGAAT
1 TTTTTGAATGAAT
2810497 AAATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTTTTGAATGAAT
Found at i:2825397 original size:35 final size:35
Alignment explanation
Indices: 2825340--2825411 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
2825330 TCGTAAGAGG
*
2825340 TCTGATTGTGTGAAGTTTTTCTGAATATATTGAAT
1 TCTGATTGTGTGAAGTTCTTCTGAATATATTGAAT
2825375 TCTGATTGTGT-AAGGTTCTTCTGAATATATTGAAT
1 TCTGATTGTGTGAA-GTTCTTCTGAATATATTGAAT
2825410 TC
1 TC
2825412 AACACTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 2 0.06
35 33 0.94
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.47
Consensus pattern (35 bp):
TCTGATTGTGTGAAGTTCTTCTGAATATATTGAAT
Found at i:2828970 original size:20 final size:19
Alignment explanation
Indices: 2828945--2828987 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
2828935 GATTATGGAT
2828945 TAATAAAAAATAAGTATAAA
1 TAATAAAAAATAA-TATAAA
*
2828965 TAATAATAAATAATATAAA
1 TAATAAAAAATAATATAAA
2828984 -AATA
1 TAATA
2828988 CTATTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 12 0.55
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
TAATAAAAAATAATATAAA
Found at i:2841487 original size:85 final size:85
Alignment explanation
Indices: 2841339--2841515 Score: 311
Period size: 85 Copynumber: 2.1 Consensus size: 85
2841329 AATTGAGCTG
* * *
2841339 AATAT-GAAAAATCAGGGTAAGGGTATCGGTACTGGAAGAACAGTACCGATACTATAGGTTTAAA
1 AATATCGAAAAATCAGGGTAAGGGTATCGGTACTGAAAGAACAATACCGACACTATAGGTTTAAA
2841403 TTTGAAGAAATACGATGAAC
66 TTTGAAGAAATACGATGAAC
*
2841423 AATATCGAAAAATCAGGGTAAGGGTATCGGTATTGAAAGAACAATACCGACACTATAGGTTTAAA
1 AATATCGAAAAATCAGGGTAAGGGTATCGGTACTGAAAGAACAATACCGACACTATAGGTTTAAA
2841488 TTTGAAGAAATACGATGAAC
66 TTTGAAGAAATACGATGAAC
2841508 AATATCGA
1 AATATCGA
2841516 CACTAATGCA
Statistics
Matches: 88, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
84 5 0.06
85 83 0.94
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (85 bp):
AATATCGAAAAATCAGGGTAAGGGTATCGGTACTGAAAGAACAATACCGACACTATAGGTTTAAA
TTTGAAGAAATACGATGAAC
Found at i:2842079 original size:54 final size:54
Alignment explanation
Indices: 2841987--2842488 Score: 700
Period size: 54 Copynumber: 9.3 Consensus size: 54
2841977 TTACAGAATG
* * * *
2841987 GGCACTATATGTGCAACCTAAGAAATTCATATTTAGTTTATGAATTTCTGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * *
2842041 GGCAGTATGTGTACAACATAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
2842095 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * **
2842149 GACACTATTTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTTGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * * *
2842203 GGCACTATATGTGCAACCAAAGAAACTCATAATAAGTTTATGAATTTCTGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * *
2842257 GGCATTATGTGTGGAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * *
2842311 GACACTATGTGTGCAACCTAAGAAATTCGTAATAAGTTTATGAATTTTCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
*
2842365 GGCACTATGTGTGCAACCTAAGAAATTCATAATTAA-TTTATGAATTTCCATATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAA-TAAGTTTATGAATTTCCGTATT
* * * * * * * * *
2842419 GGCACTATGTGTGCACCCCACGTAATTCATAGTGAGTTTTTGAATTACCGTATC
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
*
2842473 GGCACTACGTGTGCAA
1 GGCACTATGTGTGCAA
2842489 AAACCATTGA
Statistics
Matches: 398, Mismatches: 48, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
53 2 0.01
54 393 0.99
55 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (54 bp):
GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
Found at i:2845706 original size:81 final size:81
Alignment explanation
Indices: 2845599--2846176 Score: 800
Period size: 81 Copynumber: 7.1 Consensus size: 81
2845589 TTGTTTTAAA
* * * * * ** *
2845599 TAAAAGATTTATTTCCTAGATATGCATTTGACAGAAATGTGTCAATTATGTTAATTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
2845664 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
2845680 TAAAAGATTAATTACCTAGCTGTGCATCTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
2845745 TTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
2845761 TAAAAGATTAATTGCCTAGCTGTGCATCTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
2845826 TTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
2845842 TAAAAGATTAATTGCCTATCTGTGCATCTT-ACAGAAAGGTGTCAATTATGCTAGTTACATTAAA
1 TAAAAGATTAATTGCCTAGCTGTGCAT-TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
2845906 GGTTAAATACCTTTGAG
65 GGTTAAATACCTTTGAG
* *
2845923 TAAAAGATTAATTGCCTAGCCGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
2845988 GTTAAACACCTTTAAG
66 GTTAAATACCTTTGAG
* * *
2846004 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAGGAAGGTGTCAATTAT-CTAAGTTAGATGAAA
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGC-CAGTTAGATGAAA
* *
2846068 GGTTAAATAGCTTCGAG
65 GGTTAAATACCTTTGAG
* * * *
2846085 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAAAAAGGTGTCAATAATGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* * *
2846150 GCTAAATGCCTTTGGG
66 GTTAAATACCTTTGAG
*
2846166 TAAAATATTAA
1 TAAAAGATTAA
2846177 ATGCTTAACA
Statistics
Matches: 448, Mismatches: 45, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
80 3 0.01
81 443 0.99
82 2 0.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:2851868 original size:54 final size:54
Alignment explanation
Indices: 2851368--2851866 Score: 698
Period size: 54 Copynumber: 9.3 Consensus size: 54
2851358 TACAGAATGT
* * *
2851368 GCACTATGTATGCAACCTAAGAAATTCATAATTAGTTTATAAATTT-CGTATTG
1 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
*
2851421 GCACTCTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
1 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
* **
2851475 GCACTATGTGTACAACCTAAGAAATTCATAATAAGTTTATGAATTTATGTATTG
1 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
* * * * *
2851529 ACACTATGTGTGAAACTTAAGAAATTCATAATAAGTTTATGATTTTTCGTATTG
1 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
* * **
2851583 ACACTATGTGTACAACCTAAGAAATTCATAATAAGTTTATGAATTTTTGTATTG
1 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
* * *
2851637 ACACTATATGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTTCCGTATTG
1 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAA-TTTCCGTATTG
*
2851692 GCACTATGTGTACAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
1 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
* *
2851746 GCACTGTGTGTGCAACCTAAG-AATTCATAATTAGTTTATGAATTTCCGTATTG
1 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
* * * * * *
2851799 GCACTGTGTGTGCACCCCACA-TAATTCATAGTTAGTTTATGAATTTCCGTATTG
1 GCACTATGTGTGCAACCTA-AGAAATTCATAATAAGTTTATGAATTTCCGTATTG
*
2851853 GCACTTTGTGTGCA
1 GCACTATGTGTGCA
2851867 CCACTGAATT
Statistics
Matches: 406, Mismatches: 36, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
53 90 0.22
54 268 0.66
55 48 0.12
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (54 bp):
GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
Found at i:2859556 original size:19 final size:19
Alignment explanation
Indices: 2859515--2859557 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2859505 ATCATGCATG
**
2859515 TGTCTACTGCTAAGTACTG
1 TGTCTACTGCTAAGTACCA
*
2859534 TGTCTACTGCTAAGTTCCA
1 TGTCTACTGCTAAGTACCA
2859553 TGTCT
1 TGTCT
2859558 TTAGCACACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.40
Consensus pattern (19 bp):
TGTCTACTGCTAAGTACCA
Found at i:2864736 original size:145 final size:146
Alignment explanation
Indices: 2864470--2864759 Score: 501
Period size: 145 Copynumber: 2.0 Consensus size: 146
2864460 CAACATCAAC
*
2864470 ATGATCCAGGAAGGCATAAAGAACATACTCCAAAACTCCAGGTATACTCTCGATGACTTCATCCT
1 ATGATCCAGGAAGGCAGAAAGAACATACTCCAAAACTCCAGGTATACTCTCGATGACTTCATCCT
* *
2864535 CCTGAAATTGAAATAGCAGTGCCAATTTCATCCCCAACTGAGGACTATTCTAAAACAATATTTTC
66 CCTGAAATTGAAATAGCAGTGCCAATTTCATCCCCAACTCAGGACTATTCTAAAACAAAATTTTC
2864600 ACCTCCATCACCATCT
131 ACCTCCATCACCATCT
*
2864616 ATGATCCAGGAAGGCAGAAAGAACATACTCC-AAACTCCGGGTATACTCTCGATGACTTCATCCT
1 ATGATCCAGGAAGGCAGAAAGAACATACTCCAAAACTCCAGGTATACTCTCGATGACTTCATCCT
* * *
2864680 CCTGAAATTGAAATAGTAGTGCCAATTTTATCCCCAACTCAGGACTATTCTGAAACAAAATTTTC
66 CCTGAAATTGAAATAGCAGTGCCAATTTCATCCCCAACTCAGGACTATTCTAAAACAAAATTTTC
*
2864745 AGCTCCATCACCATC
131 ACCTCCATCACCATC
2864760 CATATATCTT
Statistics
Matches: 136, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
145 106 0.78
146 30 0.22
ACGTcount: A:0.34, C:0.27, G:0.13, T:0.26
Consensus pattern (146 bp):
ATGATCCAGGAAGGCAGAAAGAACATACTCCAAAACTCCAGGTATACTCTCGATGACTTCATCCT
CCTGAAATTGAAATAGCAGTGCCAATTTCATCCCCAACTCAGGACTATTCTAAAACAAAATTTTC
ACCTCCATCACCATCT
Found at i:2872333 original size:59 final size:59
Alignment explanation
Indices: 2872257--2873024 Score: 774
Period size: 59 Copynumber: 13.1 Consensus size: 59
2872247 ATGTATGGTG
* * * *
2872257 ATTTCTAGATAGAGCACTTTGTGTGCGAAAATGGTAATGAAATCATATTAAATGTATGA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
* * * * * * * *
2872316 ATTTCCATATAGGGCACTTCGTGTGCTAAAATGATATGGAAATCATATTAAGTGTATGG
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
*
2872375 ATTTCCA-ATAGAACACTTTGTGTGCTAAAATGGTAAGGAAATCATA-TAAATGTATGA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
* * * * ** *
2872432 ATTTCCAGATAGGGTACTTCGTGTGCTAAAATGATAAGGAAATCATACTAGGTGTATGG
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
* * * * *
2872491 ATTTCTAGATATAACACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATCA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
* * ** * * * *
2872550 ATTTCTAGATAGGGCACTTCATGTTCTAAAATGATAAGGATATCATACTAAGA-GTATGG
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAA-ATGTATGA
** * * * *
2872609 ATTTTAAGATAAAGCACTTTGTGTGCTAAAATGGTAAAGAAACCATATTAAATGTATGA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
* * * * * *
2872668 ATTTCTAGATAG-GGACTTTGTGTGCTAAAATGATAGGGAAATCATACTAAGTGTATGG
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
* * * * *
2872726 ATTTCCAGATAGAGCACTATATGTGCTAAAATGGTAAGGAAATCATATTAAAGGTATAA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
* * * * * **
2872785 ATTTCCAGATAGGGCACTTCGGGTGCTAAAATGATAAGGGAATCATACTATGTGTATGA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
* ** * * *
2872844 ATTTCCAGATAAAGCACTAAGTGTGCTAAAATGAG-AAGGAAATCATACTAAGTATATGG
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATG-GTAAGGAAATCATACTAAATGTATGA
* ** * * * *
2872903 ATTTCCAGACAGAGCACTAAGTGTGCTAAAACGAG-AAGGAAATCCTACTAAGTGTATGG
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATG-GTAAGGAAATCATACTAAATGTATGA
* * ** * * *
2872962 ATTTCTAGATAGAGAACTAAGTGTCCTAAAATGATAAGGAAATCATACTAAGTGTATGA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
2873021 ATTT
1 ATTT
2873025 TCGTATGGAA
Statistics
Matches: 584, Mismatches: 118, Indels: 14
0.82 0.16 0.02
Matches are distributed among these distances:
57 16 0.03
58 118 0.20
59 449 0.77
60 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.31
Consensus pattern (59 bp):
ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
Found at i:2872583 original size:118 final size:118
Alignment explanation
Indices: 2872256--2873024 Score: 978
Period size: 118 Copynumber: 6.5 Consensus size: 118
2872246 TATGTATGGT
* * *
2872256 GATTTCTAGATAGAGCACTTTGTGTGCGAAAATGGTAATGAAATCATATTAAATGTATGAATTTC
1 GATTTCTAGATAGAACACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTC
* * *
2872321 CATATAGGGCACTTCGTGTGCTAAAATGATATGGAAATCATATTAAGTGTATG
66 CAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
*
2872374 GATTTCCA-ATAGAACACTTTGTGTGCTAAAATGGTAAGGAAATCATA-TAAATGTATGAATTTC
1 GATTTCTAGATAGAACACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTC
* *
2872437 CAGATAGGGTACTTCGTGTGCTAAAATGATAAGGAAATCATACTAGGTGTATG
66 CAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
* *
2872490 GATTTCTAGATATAACACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATCAATTTC
1 GATTTCTAGATAGAACACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTC
* * * * *
2872555 TAGATAGGGCACTTCATGTTCTAAAATGATAAGGATATCATACTAAGAGTATG
66 CAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
* *
2872608 GATTT-TAAGATA-AAGCACTTTGTGTGCTAAAATGGTAAAGAAACCATATTAAATGTATGAATT
1 GATTTCT-AGATAGAA-CACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATT
* * *
2872671 TCTAGATAGGG-ACTTTGTGTGCTAAAATGATAGGGAAATCATACTAAGTGTATG
64 TCCAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
* * * * * *
2872725 GATTTCCAGATAGAGCACTATATGTGCTAAAATGGTAAGGAAATCATATTAAAGGTATAAATTTC
1 GATTTCTAGATAGAACACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTC
* * *
2872790 CAGATAGGGCACTTCGGGTGCTAAAATGATAAGGGAATCATACTATGTGTATG
66 CAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
* * ** * * * *
2872843 AATTTCCAGATA-AAGCACTAAGTGTGCTAAAATGAG-AAGGAAATCATACTAAGTATATGGATT
1 GATTTCTAGATAGAA-CACTTTGTGTGCTAAAATG-GTAAGGAAATCATATTAAATGTATGAATT
* * ** * * *
2872906 TCCAGACAGAGCACTAAGTGTGCTAAAACGAGAAGGAAATCCTACTAAGTGTATG
64 TCCAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
** * * * *
2872961 GATTTCTAGATAGAGA-ACTAAGTGTCCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTT
1 GATTTCTAGATAGA-ACACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTT
2873025 TCGTATGGAA
Statistics
Matches: 571, Mismatches: 68, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
116 71 0.12
117 177 0.31
118 320 0.56
119 2 0.00
120 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (118 bp):
GATTTCTAGATAGAACACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTC
CAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
Found at i:2872753 original size:235 final size:233
Alignment explanation
Indices: 2872256--2873024 Score: 997
Period size: 235 Copynumber: 3.3 Consensus size: 233
2872246 TATGTATGGT
* * * *
2872256 GATTTCTAGATAGAGCACTTTGTGTGCGAAAATGGTAATGAAATCATATTAAATGTATGAATTTC
1 GATTTCTAGATAGAGCACTATATGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTC
* * *
2872321 CATATAGGGCACTTCGTGTGCTAAAATGATATGGAAATCATATTAAGTGTATGGATTTCCA-ATA
66 CAGATAGGGCACTTCGTGTGCTAAAATGATAAGG-AATCATACTAAGTGTATGGATTTCCAGATA
2872385 GAA-CACTTTGTGTGCTAAAATGGTAAGGAAATCATATAAATGTATGAATTTCCAGATAGGGTAC
130 -AAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATATAAATGTATGAATTTCCAGATAGGG-AC
* *
2872449 TTCGTGTGCTAAAATGATAAGGAAATCATACTAGGTGTATG
193 TTAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
* * * * *
2872490 GATTTCTAGATATAACACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATCAATTTC
1 GATTTCTAGATAGAGCACTATATGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTC
* * * * **
2872555 TAGATAGGGCACTTCATGTTCTAAAATGATAAGGATATCATACTAAGAGTATGGATTTTAAGATA
66 CAGATAGGGCACTTCGTGTGCTAAAATGATAAGGA-ATCATACTAAGTGTATGGATTTCCAGATA
* * *
2872620 AAGCACTTTGTGTGCTAAAATGGTAAAGAAACCATATTAAATGTATGAATTTCTAGATAGGGACT
130 AAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATA-TAAATGTATGAATTTCCAGATAGGGACT
* *
2872685 TTGTGTGCTAAAATGATAGGGAAATCATACTAAGTGTATG
194 TAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
* * *
2872725 GATTTCCAGATAGAGCACTATATGTGCTAAAATGGTAAGGAAATCATATTAAAGGTATAAATTTC
1 GATTTCTAGATAGAGCACTATATGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTC
* * *
2872790 CAGATAGGGCACTTCGGGTGCTAAAATGATAAGGGAATCATACTATGTGTATGAATTTCCAGATA
66 CAGATAGGGCACTTCGTGTGCTAAAATGATAA-GGAATCATACTAAGTGTATGGATTTCCAGATA
** * * * * *
2872855 AAGCACTAAGTGTGCTAAAATGAG-AAGGAAATCATACTAAGTATATGGATTTCCAGACAGAGCA
130 AAGCACTTTGTGTGCTAAAATG-GTAAGGAAATCATA-TAAATGTATGAATTTCCAGATAG-GGA
* * * *
2872919 CTAAGTGTGCTAAAACGAGAAGGAAATCCTACTAAGTGTATG
192 CTTAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
* * * * *
2872961 GATTTCTAGATAGAGAACTA-AGTGTCCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTT
1 GATTTCTAGATAGAGCACTATA-TGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTT
2873025 TCGTATGGAA
Statistics
Matches: 466, Mismatches: 61, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
233 1 0.00
234 112 0.24
235 233 0.50
236 120 0.26
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (233 bp):
GATTTCTAGATAGAGCACTATATGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTC
CAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAATCATACTAAGTGTATGGATTTCCAGATAA
AGCACTTTGTGTGCTAAAATGGTAAGGAAATCATATAAATGTATGAATTTCCAGATAGGGACTTA
GTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
Found at i:2879082 original size:19 final size:19
Alignment explanation
Indices: 2879041--2879083 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2879031 ATCATGCATG
* *
2879041 TGTCTACTGCTATGTACCG
1 TGTCTACTGCTAAGTACCA
*
2879060 TGTCTACTGCTAAGTTCCA
1 TGTCTACTGCTAAGTACCA
2879079 TGTCT
1 TGTCT
2879084 TTAGCACACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.40
Consensus pattern (19 bp):
TGTCTACTGCTAAGTACCA
Found at i:2880450 original size:2 final size:2
Alignment explanation
Indices: 2880445--2880493 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
2880435 CGCACTGTCG
*
2880445 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CT CA CA -A CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2880486 CA CA CA CA
1 CA CA CA CA
2880494 TATATGTATG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.49, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:2880503 original size:4 final size:4
Alignment explanation
Indices: 2880496--2882596 Score: 2944
Period size: 4 Copynumber: 540.0 Consensus size: 4
2880486 CACACACATA
2880496 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2880544 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
2880592 TA-G TATG TATG TATG TATG TATG TATG TATG TCTG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2880639 TATTG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TA-TG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2880688 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
2880736 T-TG TATG TATG TAGG TA-- TATG TATG TATG --TG TATG TATG -ATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2880778 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2880826 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2880874 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2880922 --TG TATG TATG TATG TATG TATG TATG TATGG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TAT-G TATG TATG TATG TATG
2880969 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2881017 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-G
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2881064 TATG TATG T-TG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2881111 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2881159 TATG TATG TATG -ATG TA-G TATG TATG TATG TATG -ATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
2881204 TATG TATG TATG TATG TATG TAGG TATG TATG TATG TATG --TG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
2881250 TATG TATG TATG --TG TATG TATG TATG TATG TATG GATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2881296 TATG TATG TATG TATG TATG TAATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG T-ATG TATG TATG TATG TATG TATG TATG
2881345 TATG TATG -ATG TATG TATG TATG TATG TATG TATG --TG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2881390 TATG -ATG TATG TATG TATG TATAG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TAT-G TATG TATG TATG TATG TATG TATG
*
2881438 TATG TATG TATG TATG TCTG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2881486 TATG TATG TATG TATG TA-G TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
2881533 TATG TATG TATG TATG T-TG TATG TATG TATG TAGTG TGTGG TGTG TGTG
1 TATG TATG TATG TATG TATG TATG TATG TATG TA-TG TAT-G TATG TATG
2881582 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
2881630 -ATG TATG TATG TGTG TATA TAGG TATG TATG TA-G TATG TA-- TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
2881674 TATG TATG --TG TATG TATG TATG TATG TATG TATG TATG TATG TGTG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
2881720 TGTG TGTG TATG TATG TATG TATG TATG TATG --TG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
2881766 TATG TGTG TA-- TATG TATG TATG TATG TATG --TG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * * *
2881810 TATG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
2881858 TATG TATG TA-G TAT- TATG TATA TGTG TATG TATG TATG --TG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2881902 TATG TATG TATG -ATG TATG TATG TATG TATG TATG TATG T-TG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2881948 TATG TATG TATG T-TG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2881995 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-G
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
2882042 TATG -ATG TATG TATG TGTG TATG TGTG TATG --TG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2882087 TATG TAT- TATG TATG TATG TATG --TG TATG TATG TATG TAATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T-ATG TATG
*
2882133 TATG TATG TCTG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
2882181 TATG --TG TATG TATG TATG TGTG T-GG TATG --TG TATG TGTG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
2882224 --TG TATG TATG TATG TA-G TATG --TG TGTG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2882267 TATG TATG TATG TATG -ATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * *
2882314 TATG TATG TATG TATG TATG TATG TATA TGTA TATG TATA TATA T-TC
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * * ** **
2882361 TTTT TCGTG TTATAA TATT TA-A TAAA TAAA TATG ATAT- TATG TATG
1 TATG T-ATG -TAT-G TATG TATG TATG TATG TATG -TATG TATG TATG
* * * * * * *
2882407 TATG TATG TATG TA-- TATG TATA TATA T-TC TTTT TCATG T-TA TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T-ATG TATG TATG
* * * * * * * * * * ** **
2882452 TATT TA-A TATA TAT- TCTT TTTCG TGT- TATAA TATT TA-A TAAA TAAA
1 TATG TATG TATG TATG TATG TAT-G TATG TAT-G TATG TATG TATG TATG
2882498 TATG T-TG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
2882545 TATG TATG TATG TATG TATG TATG TATG TACG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2882593 TATG
1 TATG
2882597 ATAAATATGA
Statistics
Matches: 1937, Mismatches: 73, Indels: 174
0.89 0.03 0.08
Matches are distributed among these distances:
2 38 0.02
3 96 0.05
4 1760 0.91
5 42 0.02
6 1 0.00
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:2891726 original size:59 final size:59
Alignment explanation
Indices: 2891661--2892373 Score: 810
Period size: 59 Copynumber: 12.1 Consensus size: 59
2891651 ATGTATGGTG
* *
2891661 ATTTCCAGATAGAGCACTTTATGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
* * *
2891720 ATTTCCAGATAGGGCACTTTGTGTGCTAAAATGATAAGGAAATCATATTAAATGTATGA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
* * ** * * ** *
2891779 ATTTCCAGATAGGGTACTTCATGTGATAAAATGATAAGGAAATCATACTAGGTGTATGG
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
* * *
2891838 ATTTCCAGATATAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATCA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
* * * *
2891897 ATTTCCAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGA-GTATGG
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAA-ATGTATGA
** * *
2891956 ATTTTAAGATAAAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
* * * * * *
2892015 ATTTCTAGATAGGGCACTTTGTGTGCTAAAAT--TATAGGGAATCATACTAAGTTTATGG
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTA-AGGAAATCATACTAAATGTATGA
* * * * * *
2892073 ATTTTCAGATATAGCACTTTATGTGCTAAAATGGTAAGGAAATCATATTAAAGGTCTGA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
* * *
2892132 ATTTCCAGATAGAGCACTTCCG-GTGCTAAAATGATAAGGAAATCATACTAAGTGTATGA
1 ATTTCCAGATAGAGCACTT-TGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
* ** * *
2892191 ATTTCCAGATAGAACACTAAGTGTGCTAAAATGAG-AAGGAAATCATACTAAGTGTATGG
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATG-GTAAGGAAATCATACTAAATGTATGA
* * * ** * *
2892250 ATTTCTAGACAGAGCACTATGTGTGCTAAAACAAG-AAGGAAATCATACTAAGTGTATGT
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAA-TGGTAAGGAAATCATACTAAATGTATGA
* ** * *
2892309 ATTTCTAGATAGAGCACTAAGTGTGCTAAAATGATAAGGAAAT-ATTACTAAGTGTATGA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCA-TACTAAATGTATGA
2892368 ATTTCC
1 ATTTCC
2892374 GTATGAAAAA
Statistics
Matches: 556, Mismatches: 87, Indels: 22
0.84 0.13 0.03
Matches are distributed among these distances:
57 2 0.00
58 48 0.09
59 503 0.90
60 3 0.01
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (59 bp):
ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAATGTATGA
Found at i:2891817 original size:118 final size:118
Alignment explanation
Indices: 2891661--2892373 Score: 903
Period size: 118 Copynumber: 6.1 Consensus size: 118
2891651 ATGTATGGTG
** * * * *
2891661 ATTTCCAGATAGAGCACTTTATGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTCC
1 ATTTCCAGATAGAGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGATTTCC
*
2891726 AGATAGGGCACTTTGTGTGCTAAAATGATAAGGAAATCATATTAAATGTATGA
66 AGATAGAGCACTTTGTGTGCTAAAATGATAAGGAAATCATATTAAATGTATGA
* * * * *
2891779 ATTTCCAGATAGGGTACTTCATGTGATAAAATGATAAGGAAATCATACTAGGTGTATGGATTTCC
1 ATTTCCAGATAGAGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGATTTCC
* * *
2891844 AGATATAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATCA
66 AGATAGAGCACTTTGTGTGCTAAAATGATAAGGAAATCATATTAAATGTATGA
* * **
2891897 ATTTCCAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGAGTATGGATTTTA
1 ATTTCCAGATAGAGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGATTTCC
* *
2891962 AGATAAAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGA
66 AGATAGAGCACTTTGTGTGCTAAAATGATAAGGAAATCATATTAAATGTATGA
* * * * * * *
2892015 ATTTCTAGATAGGGCACTTTGTGTGCTAAAATTAT-AGGGAATCATACTAAGTTTATGGATTTTC
1 ATTTCCAGATAGAGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGATTTCC
* * * * *
2892079 AGATATAGCACTTTATGTGCTAAAATGGTAAGGAAATCATATTAAAGGTCTGA
66 AGATAGAGCACTTTGTGTGCTAAAATGATAAGGAAATCATATTAAATGTATGA
*
2892132 ATTTCCAGATAGAGCACTTCCG-GTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTC
1 ATTTCCAGATAGAGCACTT-CGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGATTTC
* ** * * * *
2892196 CAGATAGAACACTAAGTGTGCTAAAATGAGAAGGAAATCATACTAAGTGTATGG
65 CAGATAGAGCACTTTGTGTGCTAAAATGATAAGGAAATCATATTAAATGTATGA
* * ** * *
2892250 ATTTCTAGACAGAGCACTAT-GTGTGCTAAAACAAGAAGGAAATCATACTAAGTGTATGTATTTC
1 ATTTCCAGATAGAGCACT-TCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGATTTC
* ** * *
2892314 TAGATAGAGCACTAAGTGTGCTAAAATGATAAGGAAAT-ATTACTAAGTGTATGA
65 CAGATAGAGCACTTTGTGTGCTAAAATGATAAGGAAATCA-TATTAAATGTATGA
2892368 ATTTCC
1 ATTTCC
2892374 GTATGAAAAA
Statistics
Matches: 526, Mismatches: 64, Indels: 10
0.88 0.11 0.02
Matches are distributed among these distances:
117 105 0.20
118 420 0.80
119 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (118 bp):
ATTTCCAGATAGAGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGATTTCC
AGATAGAGCACTTTGTGTGCTAAAATGATAAGGAAATCATATTAAATGTATGA
Found at i:2896132 original size:20 final size:21
Alignment explanation
Indices: 2896086--2896146 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
2896076 TCCCCTGTGG
2896086 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
2896109 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
2896129 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
2896147 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:2906062 original size:20 final size:20
Alignment explanation
Indices: 2906010--2906064 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
2906000 ATCGGTAAGG
**
2906010 GGTATCGATACCATAGTATG
1 GGTATCGATACCATAGTAAA
* *
2906030 GTTGTATCTATACCATGGTAAA
1 G--GTATCGATACCATAGTAAA
2906052 GGTATCGATACCA
1 GGTATCGATACCA
2906065 GGCAATATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 12 0.43
22 16 0.57
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (20 bp):
GGTATCGATACCATAGTAAA
Found at i:2906548 original size:59 final size:59
Alignment explanation
Indices: 2906451--2907219 Score: 847
Period size: 59 Copynumber: 13.1 Consensus size: 59
2906441 ATATATGGTG
*
2906451 ATTTCCAGATAGAGCACTTTTTGTGCTAAAAT-AGTAAGGAAATCATATTTAA-TGTATGA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGA-TAAGGAAATCATA-TTAAGTGTATGA
* * * *
2906510 ATTTCTAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATATTAAGTGTATGG
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGATAAGGAAATCATATTAAGTGTATGA
* * * * *
2906569 ATTTCTAGATA-ATGCACTTT-TTTTCTAAAATTG-TAAGGAAATCATATTAAATGTTTGA
1 ATTTCCAGATAGA-GCACTTTGTGTGCTAAAA-TGATAAGGAAATCATATTAAGTGTATGA
* * * * *
2906627 ATTTTCAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGG
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGATAAGGAAATCATATTAAGTGTATGA
* * * *
2906686 A-TTCCATATAGAGCACTTTGTGTGCTAAAATGGTAAAGAAATCATATTAAATGTATGA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGATAAGGAAATCATATTAAGTGTATGA
* * * ** * *
2906744 ATTTCCAGATAGGGCACTTCGTGCGCTAAAATGATAACCAAATCATACTAAGTGTATGG
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGATAAGGAAATCATATTAAGTGTATGA
* * * *
2906803 ATTTCCAAATAGAACACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGATAAGGAAATCATATTAAGTGTATGA
* * *
2906862 ATTTCCAGATAGGGCACTTTGTGTGCT-AAATGATAAGGAAATCATACTAAGTGTATGG
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGATAAGGAAATCATATTAAGTGTATGA
* * * *
2906920 ATTTCTAGATAGAGCACTTTGTGTGCT-AAATGGTAAGGAAATTATATTAAAG-GTCTGA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGATAAGGAAATCATATT-AAGTGTATGA
* * * * * * *
2906978 ATTTCCACATAGGGAACTTCGGGTGCTAAAATGATAAGAAAATCATACTAAGTGTATGA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGATAAGGAAATCATATTAAGTGTATGA
* ** * *
2907037 ATTTCCAGATAAAGCACTAAGTGTGCTAAAATG-TGAAGGAAATCATACTAAGTGTATGG
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGAT-AAGGAAATCATATTAAGTGTATGA
* ** * * * * *
2907096 ATTTCCAGACAGAGCACTAAGTGTGCTATAATGAGAAGGAAATCATACTAAATGTTTGA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGATAAGGAAATCATATTAAGTGTATGA
* ** * * *
2907155 ATTTCCAAATAGAGCACTAAGTGTGCTAAAATGAGAATGAAATCATACTAAGTGTATGA
1 ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGATAAGGAAATCATATTAAGTGTATGA
2907214 ATTTCC
1 ATTTCC
2907220 CTATGGAAAA
Statistics
Matches: 598, Mismatches: 99, Indels: 26
0.83 0.14 0.04
Matches are distributed among these distances:
58 199 0.33
59 398 0.67
60 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (59 bp):
ATTTCCAGATAGAGCACTTTGTGTGCTAAAATGATAAGGAAATCATATTAAGTGTATGA
Found at i:2906608 original size:117 final size:118
Alignment explanation
Indices: 2906450--2907219 Score: 1023
Period size: 117 Copynumber: 6.6 Consensus size: 118
2906440 TATATATGGT
* * *
2906450 GATTTCCAGATAGAGCACTTTTTGTGCTAAAATAGTAAGGAAATCATATTTAATGTATGAATTTC
1 GATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTC
* *
2906515 TAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATATTAAGTGTATG
66 CAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
* * * * *
2906568 GATTTCTAGATA-ATGCACTTT-TTTTCTAAAATTGTAAGGAAATCATATTAAATGTTTGAATTT
1 GATTTCCAGATAGA-GCACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTT
*
2906631 TCAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
65 CCAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
* *
2906685 GA-TTCCATATAGAGCACTTTGTGTGCTAAAATGGTAAAGAAATCATATTAAATGTATGAATTTC
1 GATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTC
* **
2906749 CAGATAGGGCACTTCGTGCGCTAAAATGATAACCAAATCATACTAAGTGTATG
66 CAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
* *
2906802 GATTTCCAAATAGAACACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTC
1 GATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTC
*
2906867 CAGATAGGGCACTTTGTGTGCT-AAATGATAAGGAAATCATACTAAGTGTATG
66 CAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
* * * *
2906919 GATTTCTAGATAGAGCACTTTGTGTGCT-AAATGGTAAGGAAATTATATTAAAGGTCTGAATTTC
1 GATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTC
* * * *
2906983 CACATAGGGAACTTCGGGTGCTAAAATGATAAGAAAATCATACTAAGTGTATG
66 CAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
* * ** * * *
2907036 AATTTCCAGATAAAGCACTAAGTGTGCTAAAAT-GTGAAGGAAATCATACTAAGTGTATGGATTT
1 GATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGT-AAGGAAATCATATTAAATGTATGAATTT
* * ** * * * *
2907100 CCAGACAGAGCACTAAGTGTGCTATAATGAGAAGGAAATCATACTAAATGTTTG
65 CCAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
* * ** * * *
2907154 AATTTCCAAATAGAGCACTAAGTGTGCTAAAATGAG-AATGAAATCATACTAAGTGTATGAATTT
1 GATTTCCAGATAGAGCACTTTGTGTGCTAAAATG-GTAAGGAAATCATATTAAATGTATGAATTT
2907218 CC
65 CC
2907220 CTATGGAAAA
Statistics
Matches: 578, Mismatches: 65, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
116 65 0.11
117 288 0.50
118 224 0.39
120 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (118 bp):
GATTTCCAGATAGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTC
CAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATG
Found at i:2907006 original size:293 final size:295
Alignment explanation
Indices: 2906451--2907218 Score: 887
Period size: 293 Copynumber: 2.6 Consensus size: 295
2906441 ATATATGGTG
** * *
2906451 ATTTCCAGATAGAGCACTTTTTGTGCTAAAAT-AGTAAGGAAATCATATTTAA-TGTATGAATTT
1 ATTTCCAGATAGAGCACTTAGTGTGCTAAAATGA-TAAGGAAATCATA-CTAAGTGTATGGATTT
* * * * * * *
2906514 CTAGATAGGGCACTTCGTGTGCTAAAATGATAAGGAAATCATATTAAGTGTATGGATTTCTAGAT
64 CCAGATAGAGCACTTAGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTCCAGAT
* * * * * *
2906579 A-ATGCACTTT-TTTTCTAAAATTG-TAAGGAAATCATATTAAATGTTTGAATTT-TCAGATAGG
129 AGA-GCACTTTGTGTGCTAAAA-TGATAAGGAAATCATACTAAGTGTATGAATTTCTCAGATAGA
* * * *
2906640 GCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGATTCCATATAGAGCACTTT
192 GCACTTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTCCACATAGAGAACTTC
* * *
2906705 GTGTGCTAAAATGGTAA-AGAAATCATATTAAATGTATGA
257 GGGTGCTAAAATGATAAGA-AAATCATACTAAATGTATGA
* * * **
2906744 ATTTCCAGATAGGGCACTTCGTGCGCTAAAATGATAACCAAATCATACTAAGTGTATGGATTTCC
1 ATTTCCAGATAGAGCACTTAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGATTTCC
* * *
2906809 AAATAGAACACTTTGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTCCAGATAG
66 AGATAGAGCACTTAGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTCCAGATAG
* *
2906874 GGCACTTTGTGTGCT-AAATGATAAGGAAATCATACTAAGTGTATGGATTTCT-AGATAGAGCAC
131 AGCACTTTGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCTCAGATAGAGCAC
* * * * * *
2906937 TTTGTGTGCT-AAATGGTAAGGAAATTATATTAAAG-GTCTGAATTTCCACATAGGGAACTTCGG
196 TTCGTGTGCTAAAATGATAAGGAAATCATACT-AAGTGTATGAA-TTCCACATAGAGAACTTCGG
*
2907000 GTGCTAAAATGATAAGAAAATCATACTAAGTGTATGA
259 GTGCTAAAATGATAAGAAAATCATACTAAATGTATGA
* *
2907037 ATTTCCAGATAAAGCACTAAGTGTGCTAAAATG-TGAAGGAAATCATACTAAGTGTATGGATTTC
1 ATTTCCAGATAGAGCACTTAGTGTGCTAAAATGAT-AAGGAAATCATACTAAGTGTATGGATTTC
* * * * * *
2907101 CAGACAGAGCACTAAGTGTGCTATAATGAG-AAGGAAATCATACTAAATGTTTGAATTTCCAAAT
65 CAGATAGAGCACTTAGTGTGCTAAAATG-GTAAGGAAATCATATTAAATGTATGAATTTCCAGAT
** * *
2907165 AGAGCACTAAGTGTGCTAAAATGAGAATGAAATCATACTAAGTGTATGAATTTC
129 AGAGCACTTTGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTC
2907219 CCTATGGAAA
Statistics
Matches: 402, Mismatches: 61, Indels: 23
0.83 0.13 0.05
Matches are distributed among these distances:
292 29 0.07
293 332 0.83
294 41 0.10
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (295 bp):
ATTTCCAGATAGAGCACTTAGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGGATTTCC
AGATAGAGCACTTAGTGTGCTAAAATGGTAAGGAAATCATATTAAATGTATGAATTTCCAGATAG
AGCACTTTGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCTCAGATAGAGCAC
TTCGTGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTCCACATAGAGAACTTCGGGT
GCTAAAATGATAAGAAAATCATACTAAATGTATGA
Found at i:2915544 original size:23 final size:23
Alignment explanation
Indices: 2915499--2915546 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2915489 GGTTCTACGC
*
2915499 GGTCCTTCAGGACAATTCAATGT
1 GGTCCTTCAGGACAACTCAATGT
*
2915522 GGTCCTTCAGGA-AAGCTCTATGT
1 GGTCCTTCAGGACAA-CTCAATGT
2915545 GG
1 GG
2915547 CACTTCATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (23 bp):
GGTCCTTCAGGACAACTCAATGT
Found at i:2921613 original size:24 final size:24
Alignment explanation
Indices: 2921586--2921638 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
2921576 CAAATCTATA
*
2921586 TGGCACTTCAGTGCATATCCTACG
1 TGGCACTTCAGTGCAAATCCTACG
* *
2921610 TGGCACTTCAGTGCAAATTCTATG
1 TGGCACTTCAGTGCAAATCCTACG
2921634 TGGCA
1 TGGCA
2921639 ATTTCGACTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
TGGCACTTCAGTGCAAATCCTACG
Found at i:2932694 original size:23 final size:23
Alignment explanation
Indices: 2932633--2932706 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
2932623 AAGAGCCACA
*
2932633 TAGAA-TGTCCTGAAGGAACGCA
1 TAGAATTGTCCTGAAGGAACGCG
* * *
2932655 TAGAATTTGTCTTGAAGGATCACG
1 TAGAA-TTGTCCTGAAGGAACGCG
* *
2932679 TAGAATTGTCCCGAAGGACCGCG
1 TAGAATTGTCCTGAAGGAACGCG
2932702 TAGAA
1 TAGAA
2932707 CCCTCGACTC
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 5 0.12
23 19 0.45
24 18 0.43
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (23 bp):
TAGAATTGTCCTGAAGGAACGCG
Found at i:2937349 original size:24 final size:23
Alignment explanation
Indices: 2937307--2937374 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
2937297 ACCACATATA
*
2937307 TGTCCCGAA-GACCGTGTAGAATT
1 TGTCCCGAAGGACCGCGTAGAA-T
*
2937330 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCGCGTAGAAT
* *
2937353 TGTCCTGATGGACCGCGTAGAA
1 TGTCCCGAAGGACCGCGTAGAA
2937375 CCCTTGACTC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 29 0.74
24 10 0.26
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (23 bp):
TGTCCCGAAGGACCGCGTAGAAT
Found at i:2937615 original size:44 final size:44
Alignment explanation
Indices: 2937475--2937597 Score: 201
Period size: 44 Copynumber: 2.8 Consensus size: 44
2937465 CAACTAGACC
* * * *
2937475 AGTAATCACGTAGGTTATGTCACATAGCTTATATCTTATGTTCA
1 AGTATTCACGTAGATCATGTCACATAGCTTATATCCTATGTTCA
2937519 AGTATTCACGTAGATCATGTCACATAGCTTATATCCTATGTTCA
1 AGTATTCACGTAGATCATGTCACATAGCTTATATCCTATGTTCA
*
2937563 AGTATTCACGTAGATCATGTCACATAACTTATATC
1 AGTATTCACGTAGATCATGTCACATAGCTTATATC
2937598 GTGTTCTCAT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 74 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (44 bp):
AGTATTCACGTAGATCATGTCACATAGCTTATATCCTATGTTCA
Found at i:2943946 original size:13 final size:14
Alignment explanation
Indices: 2943912--2943945 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
2943902 CAGGTAATGG
2943912 ATTTTTTCATCTGC
1 ATTTTTTCATCTGC
2943926 ATTTTTTCATCTGC
1 ATTTTTTCATCTGC
2943940 ATTTTT
1 ATTTTT
2943946 CTTAACTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.15, C:0.18, G:0.06, T:0.62
Consensus pattern (14 bp):
ATTTTTTCATCTGC
Found at i:2947620 original size:17 final size:17
Alignment explanation
Indices: 2947598--2947667 Score: 104
Period size: 17 Copynumber: 4.1 Consensus size: 17
2947588 AATTAAGAGT
*
2947598 TAGTTTAATAAATGAAC
1 TAGTTTAATTAATGAAC
* * *
2947615 TAGTTTGATTTATTAAC
1 TAGTTTAATTAATGAAC
2947632 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
2947649 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
2947666 TA
1 TA
2947668 ACTTTATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 46 1.00
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:2947676 original size:17 final size:17
Alignment explanation
Indices: 2947601--2947677 Score: 75
Period size: 17 Copynumber: 4.5 Consensus size: 17
2947591 TAAGAGTTAG
* *
2947601 TTTAATAAATGAACTAG
1 TTTAATTAATGAACTAC
* * * *
2947618 TTTGATTTATTAACTAG
1 TTTAATTAATGAACTAC
*
2947635 TTTAATTAATGAACTAG
1 TTTAATTAATGAACTAC
2947652 TTTAATTAATGAACTAAC
1 TTTAATTAATGAACT-AC
2947670 TTT-ATTAA
1 TTTAATTAA
2947678 ATTAAATAGA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
17 47 0.92
18 4 0.08
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.44
Consensus pattern (17 bp):
TTTAATTAATGAACTAC
Found at i:2947677 original size:34 final size:34
Alignment explanation
Indices: 2947601--2947677 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
2947591 TAAGAGTTAG
* * * * *
2947601 TTTAATAAATGAACTAGTTTGATTTATTAACTAG
1 TTTAATTAATGAACTAGTTTAATTAATGAACTAC
2947635 TTTAATTAATGAACTAGTTTAATTAATGAACTAAC
1 TTTAATTAATGAACTAGTTTAATTAATGAACT-AC
2947670 TTT-ATTAA
1 TTTAATTAA
2947678 ATTAAATAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 33 0.89
35 4 0.11
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.44
Consensus pattern (34 bp):
TTTAATTAATGAACTAGTTTAATTAATGAACTAC
Found at i:2950637 original size:15 final size:15
Alignment explanation
Indices: 2950613--2950665 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
2950603 TAAAACAAGA
*
2950613 AGAAAATTAAATGCT
1 AGAAATTTAAATGCT
*
2950628 AGAAATTTAAAGGACT
1 AGAAATTTAAATG-CT
*
2950644 -GAAATTTATAATGTT
1 AGAAATTTA-AATGCT
2950659 AGAAATT
1 AGAAATT
2950666 AAAAGACGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 20 0.65
16 11 0.35
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.32
Consensus pattern (15 bp):
AGAAATTTAAATGCT
Found at i:2970223 original size:15 final size:15
Alignment explanation
Indices: 2970203--2970235 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2970193 TTAGCTGGGT
*
2970203 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
2970218 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
2970233 GGG
1 GGG
2970236 TAATGTCTCA
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:0.06, C:0.15, G:0.70, T:0.09
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:2970588 original size:25 final size:26
Alignment explanation
Indices: 2970548--2970596 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
2970538 ACAAAATAGT
2970548 AAATATTATTAAAATTAAAAAAATGA
1 AAATATTATTAAAATTAAAAAAATGA
* *
2970574 AAATATT-TTATAATTATAAAAAT
1 AAATATTATTAAAATTAAAAAAAT
2970597 ATTCAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (26 bp):
AAATATTATTAAAATTAAAAAAATGA
Found at i:2984758 original size:85 final size:85
Alignment explanation
Indices: 2984435--2984747 Score: 466
Period size: 85 Copynumber: 3.7 Consensus size: 85
2984425 AATGATGTGT
* * * *
2984435 GCTTCAATGACACGAAATGTAAGTCATATATGCGTGTCATAAATTTATGACACATAAATGTATGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTATGT
* *
2984500 CAAGCAT-ATTTATGACGGGG
66 C-ATCTTAATTTATGACGGGG
**
2984520 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGTACAAATGTATGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTATGT
*
2984585 CATCTTAATTTATGATGGGGG
66 CATCTTAATTTATGA-CGGGG
* * *
2984606 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAAAGTGTGT
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTATGT
2984671 CATCTTAATTTATGACGGGG
66 CATCTTAATTTATGACGGGG
* * *
2984691 GCTTCAATGACGCGCAATGTAAGTCATACATGTGCGTCATAGATTTATGACACACAA
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAA
2984748 TTGCGCGTCA
Statistics
Matches: 209, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
84 3 0.01
85 125 0.60
86 81 0.39
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (85 bp):
GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTATGT
CATCTTAATTTATGACGGGG
Found at i:2984782 original size:171 final size:171
Alignment explanation
Indices: 2984435--2984783 Score: 450
Period size: 171 Copynumber: 2.0 Consensus size: 171
2984425 AATGATGTGT
* * *
2984435 GCTTCAATGACACGAAATGTAAGTCATATATGCGTGTCATAAATTTATGACACATAAATGTATGT
1 GCTTCAATGACACGAAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAAAGTATGT
*
2984500 CAAGCATATTTATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATT
66 CAAGCATATTTATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGCGTCATAAATT
** * * *** * *
2984565 TATGACGTACAAATGTATGTCATCTTAATTTATGATGGGGG
131 TATGACACACAAATGCACGTCATAAAAATTCATGATCGGGG
* * * *
2984606 GCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAAAGTGTGT
1 GCTTCAATGACACGAAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAAAGTATGT
* * * *
2984671 C-ATCTTAATTTATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGTGCGTCATAGAT
66 CAAGCAT-ATTTATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGCGTCATAAAT
* * *
2984735 TTATGACACACAATTGCGCGTCATAAAAAATTCATG-TCGGTG
130 TTATGACACACAAATGCACGTCAT-AAAAATTCATGATCGGGG
2984777 GCTTCAA
1 GCTTCAA
2984784 CGATAAGAAT
Statistics
Matches: 152, Mismatches: 24, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
170 3 0.02
171 142 0.93
172 7 0.05
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (171 bp):
GCTTCAATGACACGAAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAAAGTATGT
CAAGCATATTTATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGCGTCATAAATT
TATGACACACAAATGCACGTCATAAAAATTCATGATCGGGG
Found at i:2985494 original size:53 final size:53
Alignment explanation
Indices: 2985378--2985494 Score: 121
Period size: 53 Copynumber: 2.2 Consensus size: 53
2985368 CTATGTGTAC
* * * *
2985378 TATCCGCAGTAAGTGTACAACCCACATAATTCAAAAAAGTTTATGAATGGCTG
1 TATCGGCACTAAGTGTACAACCCACAGAATTCAAAAAAGTTTATGAACGGCTG
* * ** *
2985431 TATCGACACTAAGTGTGCAACCCATGGAATTCAAAATAAGTTT-TGAAC-GATCG
1 TATCGGCACTAAGTGTACAACCCACAGAATTCAAAA-AAGTTTATGAACGGCT-G
2985484 TATCGGCACTA
1 TATCGGCACTA
2985495 CGTTTGCACC
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
52 2 0.04
53 44 0.85
54 6 0.12
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (53 bp):
TATCGGCACTAAGTGTACAACCCACAGAATTCAAAAAAGTTTATGAACGGCTG
Found at i:2987429 original size:26 final size:26
Alignment explanation
Indices: 2987382--2987431 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2987372 AAGATTTTTA
*
2987382 GTTAGTTTTTGTTTCTTGTTTTTCTT
1 GTTAGTTTTTGTTTCTTCTTTTTCTT
*
2987408 GTTA-TTTTTGTTTATTTCTTTTTC
1 GTTAGTTTTTGTTT-CTTCTTTTTC
2987432 AGGTTTTGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.06, C:0.08, G:0.12, T:0.74
Consensus pattern (26 bp):
GTTAGTTTTTGTTTCTTCTTTTTCTT
Found at i:2996367 original size:16 final size:16
Alignment explanation
Indices: 2996346--2996376 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2996336 TTTTTTACCA
2996346 CCTACCACAATAACCT
1 CCTACCACAATAACCT
*
2996362 CCTACCATAATAACC
1 CCTACCACAATAACC
2996377 GCCCATTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.19
Consensus pattern (16 bp):
CCTACCACAATAACCT
Found at i:2998193 original size:9 final size:9
Alignment explanation
Indices: 2998179--2998204 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2998169 TCACCGTGCA
2998179 TTCAATTTT
1 TTCAATTTT
2998188 TTCAATTTT
1 TTCAATTTT
2998197 TTCAATTT
1 TTCAATTT
2998205 GGTCACTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (9 bp):
TTCAATTTT
Found at i:3012227 original size:11 final size:11
Alignment explanation
Indices: 3012211--3012236 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3012201 CTTCTGCAGC
3012211 TATCTTGAGAT
1 TATCTTGAGAT
3012222 TATCTTGAGAT
1 TATCTTGAGAT
3012233 TATC
1 TATC
3012237 CTCACTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (11 bp):
TATCTTGAGAT
Found at i:3015019 original size:43 final size:43
Alignment explanation
Indices: 3014955--3015071 Score: 146
Period size: 43 Copynumber: 2.7 Consensus size: 43
3014945 CGAAGGGGCC
* * * ***
3014955 ATTTCAACTCCAAGACAGAGGATATCGTACCCATGGATCCACG
1 ATTTCAACTTCACGACGGAGGATATCGTACCCACACATCCACG
*
3014998 ATTTCAA-TTCCACGATGGAGGATATCGTACCCACACATCCACG
1 ATTTCAACTT-CACGACGGAGGATATCGTACCCACACATCCACG
*
3015041 ATTTCAACTTCACGACGAAGGATATCGTACC
1 ATTTCAACTTCACGACGGAGGATATCGTACC
3015072 AAATCTACAT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 1 0.02
43 60 0.95
44 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (43 bp):
ATTTCAACTTCACGACGGAGGATATCGTACCCACACATCCACG
Found at i:3017278 original size:15 final size:15
Alignment explanation
Indices: 3017260--3017296 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3017250 GTTTTCTTTA
3017260 TATCTATTTTTTATT
1 TATCTATTTTTTATT
*
3017275 TATCTA-ATTTTATT
1 TATCTATTTTTTATT
3017289 T-TCTATTT
1 TATCTATTT
3017297 GCTTTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
13 4 0.21
14 9 0.47
15 6 0.32
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (15 bp):
TATCTATTTTTTATT
Found at i:3017397 original size:12 final size:13
Alignment explanation
Indices: 3017366--3017397 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3017356 ATATATTTCA
3017366 TTTATTTTTCTTG
1 TTTATTTTTCTTG
3017379 TTT-TTTTTCTT-
1 TTTATTTTTCTTG
3017390 TTTATTTT
1 TTTATTTT
3017398 GTTTATTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 12 0.67
13 3 0.17
ACGTcount: A:0.06, C:0.06, G:0.03, T:0.84
Consensus pattern (13 bp):
TTTATTTTTCTTG
Found at i:3017583 original size:16 final size:16
Alignment explanation
Indices: 3017559--3017590 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3017549 TTTCATTTTA
*
3017559 CATTCTTTATTTCATT
1 CATTATTTATTTCATT
3017575 CATTATTTATTTCATT
1 CATTATTTATTTCATT
3017591 TGTTTTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.16, G:0.00, T:0.62
Consensus pattern (16 bp):
CATTATTTATTTCATT
Found at i:3035707 original size:22 final size:22
Alignment explanation
Indices: 3035682--3035725 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3035672 ATTCTAGAGC
* *
3035682 TTTAGGATGAATTTGGACTTAA
1 TTTAGGATGAATATAGACTTAA
*
3035704 TTTAGGCTGAATATAGACTTAA
1 TTTAGGATGAATATAGACTTAA
3035726 CTTCGTCCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (22 bp):
TTTAGGATGAATATAGACTTAA
Found at i:3036440 original size:17 final size:17
Alignment explanation
Indices: 3036388--3036456 Score: 68
Period size: 18 Copynumber: 3.9 Consensus size: 17
3036378 TTTAAAGAGG
3036388 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
* * *
3036405 CAATTTAAATGAATGAAC
1 TAGTTT-AATTAATGAAC
*
3036423 TAGTTTAATTAGTGAAC
1 TAGTTTAATTAATGAAC
3036440 TAGCTTT-ATTGAATGAA
1 TAG-TTTAATT-AATGAA
3036457 AGAGCGAACT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
17 19 0.46
18 22 0.54
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:3038901 original size:45 final size:44
Alignment explanation
Indices: 3038850--3039194 Score: 343
Period size: 45 Copynumber: 7.7 Consensus size: 44
3038840 ATAACATACA
* *
3038850 TTTATGTTAATAATGCACCCATATGCATTTCAATCATAATATATT
1 TTTATGTTGATAATGCACCCATATACATTTCAA-CATAATATATT
* *
3038895 TTTATGTTAATAATGCACCCATATGCATTTCAATCATAATATATT
1 TTTATGTTGATAATGCACCCATATACATTTCAA-CATAATATATT
* * * * * *
3038940 TTTATGCTGATAATGCACTCATATGCATTTCAATAATAACATACT
1 TTTATGTTGATAATGCACCCATATACATTTCAA-CATAATATATT
* * *
3038985 TTTCTGTTGATAATGTACCCATATACATTTCAACTATAATATA-C
1 TTTATGTTGATAATGCACCCATATACATTTCAAC-ATAATATATT
* * **
3039029 TTTACTGTTGATAATGTACTCATATACATTTCAACTATTGTATATT
1 TTTA-TGTTGATAATGCACCCATATACATTTCAAC-ATAATATATT
* * *
3039075 TTTCTGTTGATAATGTACCCATATACATTTCAAC-TATATCATACT
1 TTTATGTTGATAATGCACCCATATACATTTCAACATA-AT-ATATT
* * * * *
3039120 TTTCTGTTGAGAATGTACCCATATACATTTCAACTATAACATCTT
1 TTTATGTTGATAATGCACCCATATACATTTCAAC-ATAATATATT
* * *
3039165 TTCATGTTGATAATGCACCCGTATGCATTT
1 TTTATGTTGATAATGCACCCATATACATTT
3039195 TAAATTTTCA
Statistics
Matches: 259, Mismatches: 34, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
43 1 0.00
44 4 0.02
45 248 0.96
46 4 0.02
47 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.42
Consensus pattern (44 bp):
TTTATGTTGATAATGCACCCATATACATTTCAACATAATATATT
Found at i:3039043 original size:135 final size:135
Alignment explanation
Indices: 3038839--3039194 Score: 434
Period size: 135 Copynumber: 2.6 Consensus size: 135
3038829 CATTCTTACT
* * * * * *
3038839 TATAACATACATTTATGTTAATAATGCACCCATATGCATTTCAA-TCATAATATATTTTTA-TGT
1 TATAACATACTTTTCTGTTGATAATGTACCCATATACATTTCAACT-ATAATATA-CTTTACTGT
* * *
3038902 TAATAATGCACCCATATGCATTTCAA-TCATAATATATTTTTATGCTGATAATGCACTCATATGC
64 TGATAATGCACCCATATGCATTTCAACT-ATAATATATTTTTATGCTGATAATGCACCCATATAC
3038966 ATTTCAA-
128 ATTTCAAC
3038973 TAATAACATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAATATACTTTACTGTT
1 T-ATAACATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAATATACTTTACTGTT
* * * ** * * *
3039038 GATAATGTACTCATATACATTTCAACTATTGTATATTTTTCTGTTGATAATGTACCCATATACAT
65 GATAATGCACCCATATGCATTTCAACTATAATATATTTTTATGCTGATAATGCACCCATATACAT
3039103 TTCAAC
130 TTCAAC
* * * *
3039109 TATATCATACTTTTCTGTTGAGAATGTACCCATATACATTTCAACTATAACAT-CTTTTCATGTT
1 TATAACATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAATATACTTTAC-TGTT
*
3039173 GATAATGCACCCGTATGCATTT
65 GATAATGCACCCATATGCATTT
3039195 TAAATTTTCA
Statistics
Matches: 191, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
134 10 0.05
135 178 0.93
136 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.41
Consensus pattern (135 bp):
TATAACATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAATATACTTTACTGTTG
ATAATGCACCCATATGCATTTCAACTATAATATATTTTTATGCTGATAATGCACCCATATACATT
TCAAC
Found at i:3039644 original size:17 final size:16
Alignment explanation
Indices: 3039622--3039656 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
3039612 ATCGATACCT
3039622 CTACTATACTATCGGTA
1 CTACTATACTAT-GGTA
3039639 CTACTATACTATGGTA
1 CTACTATACTATGGTA
3039655 CT
1 CT
3039657 GATACTCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (16 bp):
CTACTATACTATGGTA
Found at i:3039850 original size:21 final size:21
Alignment explanation
Indices: 3039821--3039875 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
3039811 CCCTTAACCT
*
3039821 GGTATCGATACCC-CTTCCCA
1 GGTACCGATACCCTCTTCCCA
*
3039841 GGCTACCGATACCCTCTTCCTA
1 GG-TACCGATACCCTCTTCCCA
*
3039863 GGTATCGATACCC
1 GGTACCGATACCC
3039876 ATTGAATGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.07
21 20 0.67
22 8 0.27
ACGTcount: A:0.20, C:0.38, G:0.16, T:0.25
Consensus pattern (21 bp):
GGTACCGATACCCTCTTCCCA
Found at i:3044713 original size:31 final size:31
Alignment explanation
Indices: 3044670--3044733 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
3044660 TAATATTTCG
*
3044670 TTTCATTTCTGCCGTTCCTTCTTCTCTTTCTT
1 TTTCATTTCTGCCGTTCCTTCTTCT-ATTCTT
**
3044702 TTTC-TTTCTGCCGTTTTTTCTTCTATTCTT
1 TTTCATTTCTGCCGTTCCTTCTTCTATTCTT
3044732 TT
1 TT
3044734 ATTCTTCTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 7 0.24
31 18 0.62
32 4 0.14
ACGTcount: A:0.03, C:0.27, G:0.06, T:0.64
Consensus pattern (31 bp):
TTTCATTTCTGCCGTTCCTTCTTCTATTCTT
Found at i:3044736 original size:8 final size:8
Alignment explanation
Indices: 3044715--3044769 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
3044705 CTTTCTGCCG
3044715 TTTT-TTC
1 TTTTATTC
*
3044722 TTCTATTC
1 TTTTATTC
3044730 TTTTATTC
1 TTTTATTC
*
3044738 TTCTTCTTC
1 TT-TTATTC
*
3044747 TTTCATTC
1 TTTTATTC
3044755 -TTTATTTC
1 TTTTA-TTC
3044763 TTTTATT
1 TTTTATT
3044770 TATTTTTCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
7 6 0.16
8 21 0.55
9 11 0.29
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTATTC
Found at i:3046685 original size:22 final size:22
Alignment explanation
Indices: 3046650--3046706 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
3046640 CCAATTGCAA
*
3046650 CACCATACCTTGCTG-TCCCAGT
1 CACCATACCCTGCTGCT-CCAGT
*
3046672 CATCATACCCTGCTGCTCCAGT
1 CACCATACCCTGCTGCTCCAGT
3046694 CACCATACCCTGC
1 CACCATACCCTGC
3046707 CAGCTCCACC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 30 0.97
23 1 0.03
ACGTcount: A:0.19, C:0.44, G:0.12, T:0.25
Consensus pattern (22 bp):
CACCATACCCTGCTGCTCCAGT
Found at i:3048848 original size:31 final size:31
Alignment explanation
Indices: 3048777--3048841 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
3048767 GTTACATCGA
*
3048777 GGACCATATTGCAAACGGACTAAATGTTGAG
1 GGACCATATTGCAAACGGACTAAATATTGAG
*
3048808 GGACCATATTGCAAACGGACTAAATATTGGG
1 GGACCATATTGCAAACGGACTAAATATTGAG
3048839 GGA
1 GGA
3048842 TTATATTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (31 bp):
GGACCATATTGCAAACGGACTAAATATTGAG
Found at i:3050482 original size:5 final size:5
Alignment explanation
Indices: 3050472--3050525 Score: 65
Period size: 5 Copynumber: 10.6 Consensus size: 5
3050462 ATCTTTATAT
* *
3050472 TTTTA TTTTA TTTTA TTTTA TTCTA -TTTA TTCTA TTTTTA TTATTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TT-TTA TTTTA
3050523 TTT
1 TTT
3050526 CATAGTGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
4 3 0.07
5 30 0.71
6 9 0.21
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:3050493 original size:35 final size:36
Alignment explanation
Indices: 3050453--3050525 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 36
3050443 TTTTATGAAA
3050453 TTTATTAAAATCT-TTATATTTTTATT-TTATTTTAT
1 TTTATT-AAATCTATTATATTTTTATTATTATTTTAT
** * *
3050488 TTTATTCTATTTATTCTATTTTTATTATTATTTTAT
1 TTTATTAAATCTATTATATTTTTATTATTATTTTAT
3050524 TT
1 TT
3050526 CATAGTGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 3 0.09
35 18 0.56
36 11 0.34
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (36 bp):
TTTATTAAATCTATTATATTTTTATTATTATTTTAT
Found at i:3065124 original size:12 final size:12
Alignment explanation
Indices: 3065107--3065132 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3065097 TGCTTATTCC
3065107 TCCAATACTAAT
1 TCCAATACTAAT
3065119 TCCAATACTAAT
1 TCCAATACTAAT
3065131 TC
1 TC
3065133 ATTGGAGTTA
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:0.38, C:0.27, G:0.00, T:0.35
Consensus pattern (12 bp):
TCCAATACTAAT
Found at i:3077155 original size:17 final size:17
Alignment explanation
Indices: 3077128--3077172 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
3077118 CCATTCCCTT
*
3077128 TCTTT-GAGAAAAATTC
1 TCTTTCGAGAAAAACTC
3077144 TCTTTCGAGAAAAACTC
1 TCTTTCGAGAAAAACTC
3077161 T-TGTTCGAGAAA
1 TCT-TTCGAGAAA
3077173 CAAATACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (17 bp):
TCTTTCGAGAAAAACTC
Found at i:3077831 original size:17 final size:17
Alignment explanation
Indices: 3077809--3077845 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
3077799 TATTTTCCCA
*
3077809 ACAAGTAAGATTCGTAT
1 ACAAGTAAGATTCGCAT
3077826 ACAAGTAAGATTCGCAT
1 ACAAGTAAGATTCGCAT
3077843 ACA
1 ACA
3077846 TCATATTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (17 bp):
ACAAGTAAGATTCGCAT
Found at i:3079435 original size:15 final size:15
Alignment explanation
Indices: 3079415--3079446 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3079405 CATCAATTTC
*
3079415 CTAAATCATCTTTGG
1 CTAAATCAGCTTTGG
3079430 CTAAATCAGCTTTGG
1 CTAAATCAGCTTTGG
3079445 CT
1 CT
3079447 TTTCTTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (15 bp):
CTAAATCAGCTTTGG
Found at i:3081847 original size:24 final size:24
Alignment explanation
Indices: 3081815--3081869 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
3081805 TCACTATGTC
3081815 AATAACAACTCGTTGTCATCAATA
1 AATAACAACTCGTTGTCATCAATA
* *
3081839 AATAACAACTTGTTGTCATCAATT
1 AATAACAACTCGTTGTCATCAATA
3081863 AATAACA
1 AATAACA
3081870 TGTTACTCTT
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:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (24 bp):
AATAACAACTCGTTGTCATCAATA
Found at i:3102262 original size:18 final size:16
Alignment explanation
Indices: 3102234--3102281 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
3102224 CAATTGAAGA
*
3102234 AGAAGAAGAAAAAATG
1 AGAAAAAGAAAAAATG
*
3102250 GGAAAACAAGAAAAAA-G
1 AG-AAA-AAGAAAAAATG
3102267 AGAAAAAGAAAAAAT
1 AGAAAAAGAAAAAAT
3102282 AATAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
15 9 0.35
16 4 0.15
17 4 0.15
18 9 0.35
ACGTcount: A:0.73, C:0.02, G:0.21, T:0.04
Consensus pattern (16 bp):
AGAAAAAGAAAAAATG
Found at i:3103675 original size:139 final size:138
Alignment explanation
Indices: 3103251--3103898 Score: 792
Period size: 139 Copynumber: 4.6 Consensus size: 138
3103241 ATCGCCAACT
* ** *
3103251 GACCAGATCTCCTCAACACGTAGGAGTATTGTCATCCGAAGATAACCAGACTTCCTCATCATGTA
1 GACCAGATCTCCTCAACACGTAGGAGCA-TGTCATCCTCAGATAACCAGACTTCCTCATCACGTA
* * * * * *
3103316 GGAACCGAGCTGTCTCCAAATTATCCCTAAAGATGGCTAGATGTCCTCATCATATAGGAACAATG
65 GGAACCGTGTTATCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAATAATG
*
3103381 TTATCCACC
130 TCATCCACC
* * * *
3103390 GACCAGACCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGATAATCAGACTTCCTCATCAAATG
1 GACCAGATCTCCTCAACACGTAGGAGCA-TGTCATCCTCAGATAACCAGACTTCCTCATC--ACG
* * * * * *
3103455 TACGAACCGTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACATCCTTATCACGTAGGAATAA
63 TAGGAACCGTGTTATCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAATAA
*
3103520 TGTCATCCACA
128 TGTCATCCACC
* * * * * *
3103531 AACCAGACCTCCTCAAAATGTAGGAGCATCGTCATCTTCAGATAACCAGACTTCCTCATCACATA
1 GACCAGATCTCCTCAACACGTAGGAGCAT-GTCATCCTCAGATAACCAGACTTCCTCATCACGTA
* * * *
3103596 AGAACCGTGTTATCTCTAAATTATCCCTAAATAAGGCTAGACGTCCTCATCACATAGGAATAATG
65 GGAACCGTGTTATCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAATAATG
3103661 TCATCCACC
130 TCATCCACC
* * *
3103670 GACCAGATCTCCTCAACGCGTAGGAGCTGTGTCATCCTCAGATAACTAGACTTCCTCATCACGTA
1 GACCAGATCTCCTCAACACGTAGGAGC-ATGTCATCCTCAGATAACCAGACTTCCTCATCACGTA
* * * * * *
3103735 GGAATCGTGTTATCTCTAATTTATCCCTAAAGATGGCTAGATGTCCTCATAACGTAGGAATAATG
65 GGAACCGTGTTATCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAATAATG
*
3103800 TCGTCCACC
130 TCATCCACC
* * * **
3103809 GACCAGATCTCGTCAACACGTAGGAGCAGTGTCACCCTCAGACAATTAGACTTCCTCATCACGTA
1 GACCAGATCTCCTCAACACGTAGGAGCA-TGTCATCCTCAGATAACCAGACTTCCTCATCACGTA
* *
3103874 GGAATCGTGTTATCACCAAATTATC
65 GGAACCGTGTTATCTCCAAATTATC
3103899 TCCAGATTGG
Statistics
Matches: 441, Mismatches: 63, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
139 320 0.73
140 2 0.00
141 119 0.27
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (138 bp):
GACCAGATCTCCTCAACACGTAGGAGCATGTCATCCTCAGATAACCAGACTTCCTCATCACGTAG
GAACCGTGTTATCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAATAATGT
CATCCACC
Found at i:3110606 original size:20 final size:18
Alignment explanation
Indices: 3110562--3110597 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3110552 TTAAAAAAAA
* *
3110562 TGTTTTTGATTTAATTGT
1 TGTTTTTGATATAATTAT
3110580 TGTTTTTGATATAATTAT
1 TGTTTTTGATATAATTAT
3110598 ATTGTTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.14, T:0.64
Consensus pattern (18 bp):
TGTTTTTGATATAATTAT
Found at i:3119939 original size:20 final size:21
Alignment explanation
Indices: 3119902--3119962 Score: 54
Period size: 23 Copynumber: 2.9 Consensus size: 21
3119892 TTTTGGTGCA
*
3119902 GAGGGAATCGA-TCGCCCC-AT
1 GAGGGAACCGATTC-CCCCTAT
*
3119922 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCTAT
*
3119943 GAAGGGGAACTGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
3119963 CACTGTGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 14 0.41
21 4 0.12
22 1 0.03
23 15 0.44
ACGTcount: A:0.23, C:0.31, G:0.28, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCTAT
Found at i:3120691 original size:21 final size:21
Alignment explanation
Indices: 3120667--3120706 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3120657 ACCGTCAACC
*
3120667 AAATCCACTTCCAAATCCTCA
1 AAATCCAATTCCAAATCCTCA
*
3120688 AAATCCAATTCCTAATCCT
1 AAATCCAATTCCAAATCCT
3120707 AATCCCATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATCCAATTCCAAATCCTCA
Found at i:3121573 original size:17 final size:17
Alignment explanation
Indices: 3121551--3121585 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3121541 AAAAGTTTTC
*
3121551 TCTTTTCCTTTTCAAGT
1 TCTTTTCATTTTCAAGT
*
3121568 TCTTTTTATTTTCAAGT
1 TCTTTTCATTTTCAAGT
3121585 T
1 T
3121586 TTATGTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.17, G:0.06, T:0.63
Consensus pattern (17 bp):
TCTTTTCATTTTCAAGT
Found at i:3129278 original size:23 final size:23
Alignment explanation
Indices: 3129207--3129278 Score: 83
Period size: 23 Copynumber: 3.0 Consensus size: 23
3129197 TTCAACTTTT
* *
3129207 TGGATTGTTTGATTTTGTGACTT-
1 TGGATTGTTTGATTTTG-AATTTG
3129230 TGGATTGTTTGGATGTTTGAATTTG
1 TGGATTGTTT-GAT-TTTGAATTTG
*
3129255 TGGATTGATTGATTTTGAATTTG
1 TGGATTGTTTGATTTTGAATTTG
3129278 T
1 T
3129279 TTGGATTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
23 21 0.49
24 9 0.21
25 13 0.30
ACGTcount: A:0.17, C:0.01, G:0.28, T:0.54
Consensus pattern (23 bp):
TGGATTGTTTGATTTTGAATTTG
Found at i:3129283 original size:25 final size:27
Alignment explanation
Indices: 3129228--3129293 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 27
3129218 ATTTTGTGAC
*
3129228 TTTGGATTGTTTGGATGTTTGAATTTG
1 TTTGGATTGATTGGATGTTTGAATTTG
3129255 --TGGATTGATT-GAT-TTTGAATTTG
1 TTTGGATTGATTGGATGTTTGAATTTG
*
3129278 TTTGGATTTA-TGGATG
1 TTTGGATTGATTGGATG
3129294 ATGTGAACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
23 10 0.30
24 4 0.12
25 19 0.58
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (27 bp):
TTTGGATTGATTGGATGTTTGAATTTG
Found at i:3131070 original size:2 final size:2
Alignment explanation
Indices: 3131063--3131098 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3131053 ACTTGTATTC
3131063 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
3131099 TGCTCTTCTT
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:3131390 original size:17 final size:17
Alignment explanation
Indices: 3131368--3131402 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3131358 AATGTTTTAA
3131368 TTTTATTTTTTATTTTG
1 TTTTATTTTTTATTTTG
3131385 TTTTATTTTTTATTTTG
1 TTTTATTTTTTATTTTG
3131402 T
1 T
3131403 CATATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (17 bp):
TTTTATTTTTTATTTTG
Found at i:3131408 original size:17 final size:17
Alignment explanation
Indices: 3131371--3131409 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
3131361 GTTTTAATTT
**
3131371 TATTTTTTATTTTGTTT
1 TATTTTTTATTTTGTCA
3131388 TATTTTTTATTTTGTCA
1 TATTTTTTATTTTGTCA
3131405 TATTT
1 TATTT
3131410 AATGTTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (17 bp):
TATTTTTTATTTTGTCA
Found at i:3134639 original size:22 final size:24
Alignment explanation
Indices: 3134595--3134640 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
3134585 TTTAAGGGGA
3134595 TAAAAACATATATCAATAGAAAATT
1 TAAAAACATATAT-AATAGAAAATT
*
3134620 TAAAAA-ATATAT-ATATAAAAT
1 TAAAAACATATATAATAGAAAAT
3134641 ATATGGGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
24 6 0.30
25 6 0.30
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (24 bp):
TAAAAACATATATAATAGAAAATT
Found at i:3135504 original size:21 final size:21
Alignment explanation
Indices: 3135463--3135504 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3135453 GACATTGGCG
* *
3135463 CTGTTGTAACTATTGTTGAAA
1 CTGTTATAACTATTATTGAAA
3135484 CTGTTATAAC-ATTATTAGAAA
1 CTGTTATAACTATTATT-GAAA
3135505 AAAGAAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (21 bp):
CTGTTATAACTATTATTGAAA
Found at i:3136423 original size:17 final size:15
Alignment explanation
Indices: 3136389--3136438 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3136379 ACAAAAAGAA
3136389 TATTACAAAAAT--AT
1 TATTA-AAAAATAAAT
3136403 TATTAATTAAAATAAAT
1 TATTAA--AAAATAAAT
*
3136420 TATTAAATAATAAAT
1 TATTAAAAAATAAAT
3136435 TATT
1 TATT
3136439 TTCTAAGGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 17 0.55
17 8 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
TATTAAAAAATAAAT
Found at i:3136769 original size:22 final size:22
Alignment explanation
Indices: 3136741--3136786 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
3136731 ATAATACACC
3136741 ACTTTTCATTCTTGGGTTAACT
1 ACTTTTCATTCTTGGGTTAACT
*
3136763 ACTTTTCATTTTTGGGTTAACT
1 ACTTTTCATTCTTGGGTTAACT
3136785 AC
1 AC
3136787 ATGATTGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (22 bp):
ACTTTTCATTCTTGGGTTAACT
Found at i:3137345 original size:248 final size:248
Alignment explanation
Indices: 3136865--3137357 Score: 720
Period size: 248 Copynumber: 2.0 Consensus size: 248
3136855 TATCTTTCGT
* * **
3136865 TTTTATTTAATTAAGATGTAGTCACCACTAGTTAATTGTTGTTAACAATTAACTTATTAGATGAC
1 TTTTATTTAATTAAGATGTAGCCACCACGAGTTAATTGTTGTTAACAATTAACAGATTAGATGAC
* * * *
3136930 ATGGTATTTTGGTATAATCACATATTTAGTCTCTGTTATTTACATATTCTCTTAATTTAGCCCTA
66 ATGGTATTTTGGTATAATAACATATTTAGTCTCTATTATTTACATATTCTCTCAATTTAGCCATA
* * *
3136995 CATTTAATAAATTAAAATAAATTTAATGTATAGTTGAATGATGATACGTTTCACCATTCGGTTGG
131 CATTTAACAAATTAAAATAAATTTAATGCATAGTTGAATGATGATACGTTTCACCATTCGGTTGA
* * *
3137060 AGGACTAACTTTATTTTAATTTGTTAAAATAAAACAAAACAAGTCAAATTAGG
196 AGGACTAAATTCATTTTAATTTGTTAAAATAAAACAAAACAAATCAAATTAGG
* * * *
3137113 TTTTATTTAATTAAGATGTGGCCACCACGAGTTAATTGTTGTTAACATTTAACAGATTAGGTGAT
1 TTTTATTTAATTAAGATGTAGCCACCACGAGTTAATTGTTGTTAACAATTAACAGATTAGATGAC
* * * *
3137178 GTGGTATTTTGGTATAATAACATATTTAGTCTCTATTATTTATATATTGTCTCAATTTAGTCATA
66 ATGGTATTTTGGTATAATAACATATTTAGTCTCTATTATTTACATATTCTCTCAATTTAGCCATA
*
3137243 CATTTAACAAATTAAAATAAATTTAAT-CATCCAGTTGAATGATGATACTTTTCACCATTCGGTT
131 CATTTAACAAATTAAAATAAATTTAATGCAT--AGTTGAATGATGATACGTTTCACCATTCGGTT
* **
3137307 GAAGGACTAAATTCATTTTTATTTGTTGTAAT-AAACAAAACAAATCAAATT
194 GAAGGACTAAATTCATTTTAATTTGTTAAAATAAAACAAAACAAATCAAATT
3137358 GAGGCTGAAG
Statistics
Matches: 217, Mismatches: 26, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
247 2 0.01
248 158 0.73
249 57 0.26
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (248 bp):
TTTTATTTAATTAAGATGTAGCCACCACGAGTTAATTGTTGTTAACAATTAACAGATTAGATGAC
ATGGTATTTTGGTATAATAACATATTTAGTCTCTATTATTTACATATTCTCTCAATTTAGCCATA
CATTTAACAAATTAAAATAAATTTAATGCATAGTTGAATGATGATACGTTTCACCATTCGGTTGA
AGGACTAAATTCATTTTAATTTGTTAAAATAAAACAAAACAAATCAAATTAGG
Found at i:3140780 original size:59 final size:59
Alignment explanation
Indices: 3140670--3140791 Score: 154
Period size: 59 Copynumber: 2.1 Consensus size: 59
3140660 AAGCAAGCTG
** * * *
3140670 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGAGGACACGACCTTATGTGT
* ** * *
3140729 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGAGGACATGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGAGGACACGACCTTATGTGT
3140788 CATA
1 CATA
3140792 CTTAGGATAG
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGAGGACACGACCTTATGTGT
Found at i:3145236 original size:14 final size:14
Alignment explanation
Indices: 3145217--3145245 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3145207 AAGGAAGTCT
3145217 ACAGTTAAGGCGTG
1 ACAGTTAAGGCGTG
3145231 ACAGTTAAGGCGTG
1 ACAGTTAAGGCGTG
3145245 A
1 A
3145246 GTACGTCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.21
Consensus pattern (14 bp):
ACAGTTAAGGCGTG
Found at i:3148275 original size:20 final size:20
Alignment explanation
Indices: 3148250--3148319 Score: 140
Period size: 20 Copynumber: 3.5 Consensus size: 20
3148240 TTTGGGGTAC
3148250 CGATTCCCCCTACAGGGAAT
1 CGATTCCCCCTACAGGGAAT
3148270 CGATTCCCCCTACAGGGAAT
1 CGATTCCCCCTACAGGGAAT
3148290 CGATTCCCCCTACAGGGAAT
1 CGATTCCCCCTACAGGGAAT
3148310 CGATTCCCCC
1 CGATTCCCCC
3148320 ACTGTTCACA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.23, C:0.39, G:0.19, T:0.20
Consensus pattern (20 bp):
CGATTCCCCCTACAGGGAAT
Found at i:3148338 original size:13 final size:13
Alignment explanation
Indices: 3148320--3148353 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3148310 CGATTCCCCC
3148320 ACTGTTCACAGGT
1 ACTGTTCACAGGT
*
3148333 ACTGTTCACGGGT
1 ACTGTTCACAGGT
*
3148346 ACTATTCA
1 ACTGTTCA
3148354 GTATTCATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (13 bp):
ACTGTTCACAGGT
Found at i:3156119 original size:42 final size:42
Alignment explanation
Indices: 3156055--3156174 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
3156045 TTTCCCCGAA
* *
3156055 TTCCAGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
3156097 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
3156139 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
3156175 TGTAATTCAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:3156389 original size:21 final size:20
Alignment explanation
Indices: 3156363--3156409 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
3156353 TAATTATTAA
*
3156363 AATATTTAAAATATATTTATT
1 AATATTTAAAATA-ATATATT
*
3156384 AATATTTATAATAATATATT
1 AATATTTAAAATAATATATT
3156404 -ATATTT
1 AATATTT
3156410 TTAATATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.25
20 6 0.25
21 12 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATTTAAAATAATATATT
Found at i:3156406 original size:29 final size:29
Alignment explanation
Indices: 3156374--3156499 Score: 88
Period size: 29 Copynumber: 4.4 Consensus size: 29
3156364 ATATTTAAAA
3156374 TATATTTATTAATATTTATAATAATATAT
1 TATATTTATTAATATTTATAATAATATAT
*
3156403 TATATTT-TTAATATTATAAAATAATCA-AT
1 TATATTTATTAATATT-TATAATAAT-ATAT
*
3156432 TATA-TTA-TAATA--TATAGATATTATAT
1 TATATTTATTAATATTTATA-ATAATATAT
* * * *
3156458 TTTA-TT-TTAATAATATATAATAATTTTTT
1 TATATTTATTAAT-ATTTATAATAA-TATAT
*
3156487 TATATTTAATAAT
1 TATATTTATTAAT
3156500 GATATATTTA
Statistics
Matches: 76, Mismatches: 9, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
25 4 0.05
26 15 0.20
27 1 0.01
28 18 0.24
29 31 0.41
30 3 0.04
31 4 0.05
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (29 bp):
TATATTTATTAATATTTATAATAATATAT
Found at i:3156409 original size:19 final size:20
Alignment explanation
Indices: 3156363--3156420 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
3156353 TAATTATTAA
* *
3156363 AATATTTAAAATATATTTATT
1 AATATTTATAATA-ATATATT
3156384 AATATTTATAATAATATATT
1 AATATTTATAATAATATATT
* *
3156404 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
3156421 AAATAATCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 15 0.45
20 6 0.18
21 12 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATTTATAATAATATATT
Found at i:3156766 original size:20 final size:20
Alignment explanation
Indices: 3156688--3156757 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
3156678 TTTCCAGATG
3156688 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
3156708 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
3156728 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
3156748 TTTTCCAGAA
1 TTTTCCAGAA
3156758 TTCAAATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:3156766 original size:40 final size:40
Alignment explanation
Indices: 3156688--3156766 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
3156678 TTTCCAGATG
* **
3156688 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
3156728 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
3156767 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:3156776 original size:15 final size:15
Alignment explanation
Indices: 3156740--3156821 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
3156730 TTACAGAAAT
**
3156740 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
3156755 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
3156769 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
3156784 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
3156799 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
3156814 GTAATTCA
1 GTAATTCA
3156822 TTTTCTGGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:3156792 original size:30 final size:30
Alignment explanation
Indices: 3156740--3156821 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
3156730 TTACAGAAAT
3156740 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
3156769 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
3156799 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
3156822 TTTTCTGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:3156814 original size:45 final size:44
Alignment explanation
Indices: 3156740--3156826 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
3156730 TTACAGAAAT
**
3156740 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
3156784 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTC
3156827 TGGAAAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Done.