Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold446
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: 3567220
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 22
Found at i:89966 original size:15 final size:15
Alignment explanation
Indices: 89918--89966 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
89908 AATCTAATTT
89918 GATTTGAATTAATCA
1 GATTTGAATTAATCA
* **
89933 GA-TTAAATTTAATTT
1 GATTTGAA-TTAATCA
89948 GATTTGAATTAATCA
1 GATTTGAATTAATCA
89963 GATT
1 GATT
89967 AAAGATAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 4 0.15
15 18 0.69
16 4 0.15
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (15 bp):
GATTTGAATTAATCA
Found at i:90009 original size:18 final size:21
Alignment explanation
Indices: 89991--90028 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
89981 TTAAAAAAAT
89991 AAAA-TTTTTAA-ATTTAATA
1 AAAATTTTTTAATATTTAATA
90010 AAAATTTTTTAATATTTAA
1 AAAATTTTTTAATATTTAA
90029 ACATAATCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 7 0.41
21 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AAAATTTTTTAATATTTAATA
Found at i:90517 original size:20 final size:21
Alignment explanation
Indices: 90488--90538 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
90478 GATTTTAAGT
*
90488 AAAATATAAAATTATTTTA-A
1 AAAATTTAAAATTATTTTATA
*
90508 AAAATTT-AAATTTTTTTATTA
1 AAAATTTAAAATTATTTTA-TA
90529 AAAATTTAAA
1 AAAATTTAAA
90539 TTTTATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 10 0.38
20 6 0.23
21 8 0.31
22 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAATTTAAAATTATTTTATA
Found at i:90518 original size:19 final size:20
Alignment explanation
Indices: 90496--90540 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
90486 GTAAAATATA
90496 AAATTATTTTA-AAAAATTT
1 AAATTATTTTATAAAAATTT
*
90515 AAATTTTTTTATTAAAAATTT
1 AAATTATTTTA-TAAAAATTT
90536 AAATT
1 AAATT
90541 TTATAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.43
21 13 0.57
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AAATTATTTTATAAAAATTT
Found at i:92237 original size:16 final size:16
Alignment explanation
Indices: 92218--92275 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
92208 AAAATTGTAA
*
92218 ATTTTTTATTATATAT
1 ATTTTTAATTATATAT
92234 A-TTTTAATT-TA-AT
1 ATTTTTAATTATATAT
*
92247 ATCTTTAATTAT-TATT
1 ATTTTTAATTATATA-T
*
92263 ATTTTTTATTATA
1 ATTTTTAATTATA
92276 ATTTACCTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
13 3 0.09
14 9 0.27
15 9 0.27
16 12 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTTTAATTATATAT
Found at i:92242 original size:29 final size:30
Alignment explanation
Indices: 92177--92267 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 30
92167 AATATAAATA
*
92177 TAAATTTAATATATATTTTATTA-ATA-ATTT
1 TAAATTT-A-ATATCTTTTATTATATATATTT
*
92207 TAAAATTGTAA-ATTTTTTATTATATATATTT
1 T-AAATT-TAATATCTTTTATTATATATATTT
*
92238 T-AATTTAATATCTTTAATTAT-TATTATTT
1 TAAATTTAATATCTTTTATTATATA-TATTT
92267 T
1 T
92268 TTATTATAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
28 5 0.10
29 30 0.58
30 5 0.10
31 11 0.21
32 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (30 bp):
TAAATTTAATATCTTTTATTATATATATTT
Found at i:92356 original size:21 final size:21
Alignment explanation
Indices: 92326--92401 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
92316 TATTCATCAT
*
92326 TAAT-TTTAATCTTATTATTA
1 TAATATTTAATATTATTATTA
92346 TAATATTTAATATTATTATTA
1 TAATATTTAATATTATTATTA
* *
92367 TTATATTATTTAATTTTACTATTA
1 -TA-A-TATTTAATATTATTATTA
* *
92391 AAATAATTAAT
1 TAATATTTAAT
92402 TTCAACCTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
20 4 0.09
21 22 0.47
22 3 0.06
23 2 0.04
24 16 0.34
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATATTTAATATTATTATTA
Found at i:92369 original size:24 final size:24
Alignment explanation
Indices: 92337--92390 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
92327 AATTTTAATC
92337 TTATTATTATAATATTTAATATTA
1 TTATTATTATAATATTTAATATTA
* *
92361 TTATTATTATATTATTTAATTTTA
1 TTATTATTATAATATTTAATATTA
*
92385 CTATTA
1 TTATTA
92391 AAATAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
TTATTATTATAATATTTAATATTA
Found at i:92780 original size:56 final size:56
Alignment explanation
Indices: 92704--92813 Score: 134
Period size: 56 Copynumber: 2.0 Consensus size: 56
92694 TAATATAAAT
*
92704 TATTAATATATTAAAATTTATT-TAAATTAAATTTGATAAT-TTATATATTTATATTA
1 TATTAATATATTAAAATTTATTAT-AATTAAATTT-AAAATATTATATATTTATATTA
** * * *
92760 TATTAATATATTTTATTTTATTATAATTATATTTAAAATATTTTATATTTATAT
1 TATTAATATATTAAAATTTATTATAATTAAATTTAAAATATTATATATTTATAT
92814 AAATTTAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
55 4 0.09
56 41 0.89
57 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (56 bp):
TATTAATATATTAAAATTTATTATAATTAAATTTAAAATATTATATATTTATATTA
Found at i:92803 original size:30 final size:30
Alignment explanation
Indices: 92743--92815 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
92733 AATTTGATAA
* *
92743 TTTATATAT-TTAT-ATTATATTAATATAT
1 TTTATATTTATTATAATTATATTAAAATAT
92771 TTTAT-TTTATTATAATTATATTTAAAATAT
1 TTTATATTTATTATAATTATA-TTAAAATAT
92801 TTTATATTTA-TATAA
1 TTTATATTTATTATAA
92816 ATTTAATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 2 0.05
28 9 0.23
29 6 0.15
30 18 0.46
31 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTATATTTATTATAATTATATTAAAATAT
Found at i:94509 original size:14 final size:14
Alignment explanation
Indices: 94438--94509 Score: 51
Period size: 14 Copynumber: 5.0 Consensus size: 14
94428 AACAAAAAAT
94438 TTAAAAAAATTATAA
1 TTAAAAAAATT-TAA
* *
94453 TTTAATAGAATTT-A
1 -TTAAAAAAATTTAA
*
94467 TTAAAAAATATTT-T
1 TTAAAAAA-ATTTAA
94481 TTAATAAATAA-TTAA
1 TTAA-AAA-AATTTAA
94496 TTAAAAAAATTTAA
1 TTAAAAAAATTTAA
94510 AGACCCCGAC
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
13 8 0.18
14 18 0.40
15 9 0.20
16 10 0.22
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (14 bp):
TTAAAAAAATTTAA
Found at i:107016 original size:21 final size:21
Alignment explanation
Indices: 106982--107022 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
106972 ACAATTAAAA
*
106982 ATAATTTATTATTAATATTTAT
1 ATAATTTATAATTAA-ATTTAT
107004 ATAA-TTATAATTAAATTTA
1 ATAATTTATAATTAAATTTA
107023 AATAGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATAATTTATAATTAAATTTAT
Found at i:107176 original size:23 final size:22
Alignment explanation
Indices: 107149--107193 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
107139 ATATATAAAT
107149 AAATCTATTTTAAAAAAGTGAAC
1 AAATCTATTTTAAAAAAG-GAAC
*
107172 AAATCTATTTTAGAAAAGGAAC
1 AAATCTATTTTAAAAAAGGAAC
107194 TCAGAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (22 bp):
AAATCTATTTTAAAAAAGGAAC
Found at i:107638 original size:20 final size:20
Alignment explanation
Indices: 107598--107638 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
107588 TATAATTAAA
*
107598 TTTAAATAAAAATATAATAT
1 TTTAAATAAAAAAATAATAT
* *
107618 TTTAATTAAAAAAATATTAT
1 TTTAAATAAAAAAATAATAT
107638 T
1 T
107639 CCAAGCCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTAAATAAAAAAATAATAT
Found at i:108392 original size:21 final size:21
Alignment explanation
Indices: 108366--108415 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
108356 AGACCAATTC
108366 AATAAAAAATAATTACGA-AAA
1 AATAAAAAA-AATTACGATAAA
* **
108387 AATAAATAAAATTATTATAAA
1 AATAAAAAAAATTACGATAAA
108408 AATAAAAA
1 AATAAAAA
108416 TTAAAAGATG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (21 bp):
AATAAAAAAAATTACGATAAA
Found at i:108918 original size:2 final size:2
Alignment explanation
Indices: 108911--108961 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
108901 AACGTAGCCT
108911 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
108953 TG TA TA TA T
1 TA TA TA TA T
108962 GAGGTTGTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:114113 original size:68 final size:68
Alignment explanation
Indices: 113958--114095 Score: 249
Period size: 68 Copynumber: 2.0 Consensus size: 68
113948 AGATCGCAAA
* *
113958 AAGAAATGTAACAAGCATAATATGACAACGGTAACACTTTTCAATTGAACTTCCAATGTATATGG
1 AAGAAATGTAACAAACATAATATGACAACGGTAACACTTTTCAATTGAACTTCCAATGTACATGG
114023 CAT
66 CAT
*
114026 AAGAAATGTAACAAACATAATATGACAATGGTAACACTTTTCAATTGAACTTCCAATGTACATGG
1 AAGAAATGTAACAAACATAATATGACAACGGTAACACTTTTCAATTGAACTTCCAATGTACATGG
114091 CAT
66 CAT
114094 AA
1 AA
114096 TATCTTTGTA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.28
Consensus pattern (68 bp):
AAGAAATGTAACAAACATAATATGACAACGGTAACACTTTTCAATTGAACTTCCAATGTACATGG
CAT
Found at i:115043 original size:19 final size:19
Alignment explanation
Indices: 115019--115064 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
115009 GTTTGCTGAG
* * * *
115019 TAATTTTTTAATTATTTAT
1 TAATTTTATAAATATTAAA
115038 TAATTTTATAAATATTAAA
1 TAATTTTATAAATATTAAA
115057 TAATTTTA
1 TAATTTTA
115065 AATTTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TAATTTTATAAATATTAAA
Found at i:118928 original size:18 final size:18
Alignment explanation
Indices: 118905--118967 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
118895 TATCTAAAAA
118905 ATAAAAAA-T-TATTTAT
1 ATAAAAAATTATATTTAT
* *
118921 ATATAAAAATTATCTTTAA
1 ATA-AAAAATTATATTTAT
* *
118940 ATTAAAAATAATATTTAT
1 ATAAAAAATTATATTTAT
118958 ATAAAAAATT
1 ATAAAAAATT
118968 TTTAAAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
16 3 0.08
17 5 0.14
18 21 0.58
19 7 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAAAAAATTATATTTAT
Found at i:120402 original size:24 final size:22
Alignment explanation
Indices: 120363--120414 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 22
120353 TTTTTGGTTG
*
120363 ATGAGAGGAGAGAAGAAAAGAA
1 ATGAGAGGAAAGAAGAAAAGAA
120385 ATGAGAGAGAAAGAAAGAAAAGAA
1 ATGAGAG-GAAAG-AAGAAAAGAA
120409 AGTGAG
1 A-TGAG
120415 TAAAGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 7 0.27
23 4 0.15
24 11 0.42
25 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.35, T:0.06
Consensus pattern (22 bp):
ATGAGAGGAAAGAAGAAAAGAA
Found at i:121536 original size:81 final size:80
Alignment explanation
Indices: 121440--122039 Score: 439
Period size: 81 Copynumber: 7.4 Consensus size: 80
121430 AAATTTTGAT
* * *
121440 TTTTTAGAAGGTAAAAATGGGGTTGGAGTATCCTTTCGGAGATGGAGGGATTGGAGTATTCCCGA
1 TTTTTAGAA-GTAAAAATGGGGTTGGAGTATCCTTTCAGAAATGGAGGGGTTGGAGTA-TCCCGA
*
121505 AGATGGAAAATTGGATA
64 AGATGGAAAATTAGATA
* * * * * * *
121522 ATTTTAGAAGTAAAAAGGGGGTTAGAGTAT-CTTCTAAGAAAT-AATGGAGTTGGAGTAACCTCG
1 TTTTTAGAAGTAAAAATGGGGTTGGAGTATCCTT-TCAGAAATGGA-GGGGTTGGAGTATCC-CG
* * *
121585 AAAAT-GAAAATTTAAATTT
63 AAGATGGAAAA-TTAGA-TA
* ** * * * *
121604 TTTTTAGAGGTAAAAATGGGGTTGGAGTATCCCCTCAGAGAT-AATGGGGTTTGAGCATCCCTGA
1 TTTTTAGAAGTAAAAATGGGGTTGGAGTATCCTTTCAGAAATGGA-GGGGTTGGAGTATCCC-GA
* *
121668 AGATGAAAAATAAGATA
64 AGATGGAAAATTAGATA
** * * * * *
121685 TTTTTAGAAGTAAAAACAGGGTTGGAGTATCC--CCGAAAATATGGTGGGGTTGGAGTAACCTAG
1 TTTTTAGAAGTAAAAATGGGGTTGGAGTATCCTTTC-AGAA-ATGGAGGGGTTGGAGTATCC-CG
* * *
121748 AAAAT-GAAAATTTTGATT
63 AAGATGGAAAA-TTAGATA
* ** ** * * *
121766 TTTTTAGAGGTAAAAACAGGGTTGGAGTATCCCCTCAGAGATGGCGGGGTTGGAGTATCCCCAAA
1 TTTTTAGAAGTAAAAATGGGGTTGGAGTATCCTTTCAGAAATGGAGGGGTTGGAGTAT-CCCGAA
*
121831 GATGGAAAATTTGATA
65 GATGGAAAATTAGATA
* ** * * *
121847 TTTTTAGAAGTAAAAACGGAATTGGAGTATTCC-TTAAGAAATGGTGGGGTTGGAGTATCCCAAA
1 TTTTTAGAAGTAAAAATGGGGTTGGAGTA-TCCTTTCAGAAATGGAGGGGTTGGAGTATCCCGAA
* *
121911 AATGAAAAAAATTA-AT-
65 GATG--GAAAATTAGATA
* * * *
121927 TTTTTAGAGGTAAAAATAGGGTTGGAGTAT-CTCTTCAGAAATGGCGAGGTTGGAGTATTCCCGA
1 TTTTTAGAAGTAAAAATGGGGTTGGAGTATCCT-TTCAGAAATGGAGGGGTTGGAGTA-TCCCGA
*
121991 AGATGGAAAATTAGGTA
64 AGATGGAAAATTAGATA
* *
122008 TTTTTAGATGTAAAAATGGGGTTGGAATATCC
1 TTTTTAGAAGTAAAAATGGGGTTGGAGTATCC
122040 CCAAAAATAA
Statistics
Matches: 408, Mismatches: 84, Indels: 52
0.75 0.15 0.10
Matches are distributed among these distances:
78 1 0.00
79 9 0.02
80 72 0.18
81 238 0.58
82 82 0.20
83 6 0.01
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.29
Consensus pattern (80 bp):
TTTTTAGAAGTAAAAATGGGGTTGGAGTATCCTTTCAGAAATGGAGGGGTTGGAGTATCCCGAAG
ATGGAAAATTAGATA
Found at i:121857 original size:162 final size:162
Alignment explanation
Indices: 121423--122041 Score: 715
Period size: 162 Copynumber: 3.8 Consensus size: 162
121413 AGTATCCCAA
* ** * *
121423 AAAATGAAAATTTTGA-TTTTTTAGAAGGTAAAAATGGGGTTGGAGTATCCTTTCGGAGATGGAG
1 AAAATGAAAATTTTGATTTTTTTAG-AGGTAAAAATAGGGTTGGAGTATCCCCTCAGAGATGGCG
* * * * * *
121487 GGATTGGAGTATTCCCGAAGATGGAAAATTGGATAATTTTAGAAGTAAAAAGGGGGTTAGAGTAT
65 GGGTTGGAGTATCCCCGAAGATGGAAAATTAGATATTTTTAGAAGTAAAAACGGGGTTGGAGTAT
** ** * *
121552 CTTCTAAGAAATAATGGAGTTGGAGTAACCTCG
130 CCCCTAAGAAATGGTGGGGTTGGAGTAACCTAG
** * ***
121585 AAAATGAAAATTTAAATTTTTTTTAGAGGTAAAAATGGGGTTGGAGTATCCCCTCAGAGATAATG
1 AAAATGAAAATTTTGA-TTTTTTTAGAGGTAAAAATAGGGTTGGAGTATCCCCTCAGAGATGGCG
* * * * * *
121650 GGGTTTGAGCATCCCTGAAGATGAAAAATAAGATATTTTTAGAAGTAAAAACAGGGTTGGAGTAT
65 GGGTTGGAGTATCCCCGAAGATGGAAAATTAGATATTTTTAGAAGTAAAAACGGGGTTGGAGTAT
*
121715 CCCCGAA-AATATGGTGGGGTTGGAGTAACCTAG
130 CCCCTAAGAA-ATGGTGGGGTTGGAGTAACCTAG
*
121748 AAAATGAAAATTTTGATTTTTTTAGAGGTAAAAACAGGGTTGGAGTATCCCCTCAGAGATGGCGG
1 AAAATGAAAATTTTGATTTTTTTAGAGGTAAAAATAGGGTTGGAGTATCCCCTCAGAGATGGCGG
* * ** *
121813 GGTTGGAGTATCCCCAAAGATGGAAAATTTGATATTTTTAGAAGTAAAAACGGAATTGGAGTATT
66 GGTTGGAGTATCCCCGAAGATGGAAAATTAGATATTTTTAGAAGTAAAAACGGGGTTGGAGTATC
* * *
121878 CCTTAAGAAATGGTGGGGTTGGAGTATCCCA-
131 CCCTAAGAAATGGTGGGGTTGGAGTAACCTAG
** * * * *
121909 AAAATGAAAAAAATT-AATTTTTTAGAGGTAAAAATAGGGTTGGAGTATCTCTTCAGAAATGGCG
1 AAAATG-AAAATTTTGATTTTTTTAGAGGTAAAAATAGGGTTGGAGTATCCCCTCAGAGATGGCG
* * * * * *
121973 AGGTTGGAGTATTCCCGAAGATGGAAAATTAGGTATTTTTAGATGTAAAAATGGGGTTGGAATAT
65 GGGTTGGAGTATCCCCGAAGATGGAAAATTAGATATTTTTAGAAGTAAAAACGGGGTTGGAGTAT
122038 CCCC
130 CCCC
122042 AAAAATAAAA
Statistics
Matches: 384, Mismatches: 68, Indels: 11
0.83 0.15 0.02
Matches are distributed among these distances:
161 107 0.28
162 144 0.38
163 125 0.33
164 8 0.02
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.29
Consensus pattern (162 bp):
AAAATGAAAATTTTGATTTTTTTAGAGGTAAAAATAGGGTTGGAGTATCCCCTCAGAGATGGCGG
GGTTGGAGTATCCCCGAAGATGGAAAATTAGATATTTTTAGAAGTAAAAACGGGGTTGGAGTATC
CCCTAAGAAATGGTGGGGTTGGAGTAACCTAG
Found at i:123213 original size:61 final size:61
Alignment explanation
Indices: 123135--123976 Score: 785
Period size: 61 Copynumber: 13.7 Consensus size: 61
123125 AAGTGTCTTA
* * * * *
123135 CTCTTTGAGGACTAAAAGGTGTCACCAACTTATATGGGCTTTAAAAGAAAAAGGCGTCATG
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCATCCTG
* * * * * *
123196 TTCTTTGATGACTAAAAGGTGTCACCAACTTGTGTGGGCTTTAAAAGGAAAATGCATCATG
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCATCCTG
* * * ** * ** * *
123257 CTTTTTGAGGGCTAAAAGTTGCCTTCAACTTGTGTGGGCTTTAAAAGAAAAAAAAAGTGTTCTA
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG---AAAAAGGCATCCTG
* * *
123321 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCCTA
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCATCCTG
* * * * * * *
123382 CTCTTTAAAGACTAAAAGGTGTCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCTTA
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCATCCTG
* * * * * * * * * *
123443 CTTTTTAAAGA-TTAAAGGTGCCACCAGCTTGTGTGGCCTTTAAAAGAAAAAAGAATCTTA
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCATCCTG
* * * * * ** *
123503 CTCTTTGAGGACTAAAAAGTGCCACTAGCTTATGTAGGCTTTAAAAGAAAAAAGAAAGTGTCCTA
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG-AAAAAG---GCATCCTG
* ** * * * * *
123568 CTTTTTGAGGACTAAAATATGCCACCAATTTGTATAGGCTTTGAAAGAAAAAGGCATCATG
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCATCCTG
* *
123629 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGACTTTGAAAAG-AAAAGGCATCCTA
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAGGCATCCTG
* * *
123690 CTCTTTGAGGAATAAAAGGTGCCACCAACTTGTATGGGCTTTAAAA-AGAAAAGGTATCCTG
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA-AAAAGGCATCCTG
* * * * * * *
123751 CTCTTTGAAGACT-AAAGGTGCCACCAGCTTATATGAGCTTTAAAAAGAAAAA-GAATCTTG
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAGGCATCCTG
* * * * * ***
123811 CTCTTTGAGGATTAAAAGGTGTCACCAGCTTGTTTGGGCTTTAAAAGGAAAAGATGTCCTG
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCATCCTG
* * * *
123872 CTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAAATGCATCCTT
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCATCCTG
* * * * *
123933 CTCTTTGAGGACAAAAATGTACCACCAGCTTGTGTGGGGTTTAA
1 CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAA
123977 GAGGGAAAAA
Statistics
Matches: 647, Mismatches: 119, Indels: 30
0.81 0.15 0.04
Matches are distributed among these distances:
60 104 0.16
61 436 0.67
62 10 0.02
64 54 0.08
65 43 0.07
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.28
Consensus pattern (61 bp):
CTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCATCCTG
Found at i:123577 original size:247 final size:245
Alignment explanation
Indices: 123133--123923 Score: 864
Period size: 247 Copynumber: 3.2 Consensus size: 245
123123 GAAAGTGTCT
* * * * *
123133 TACTCTTTGAGGACTAAAAGGTGTCACCAACTTATATGGGCTTTAAAAGAAAAAGGCGTCAT-GT
1 TACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCATACT
* * * * * *
123197 TCTTTGATGACTAAAAGGTGTCACCAACTTGTGTGGGCTTTAAAAGGAAAATGCATCATGCTTTT
66 T-TTTGAAGA-TAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAAGAATCATGCTCTT
* * * * *
123262 TGAGGGCTAAAAGTTGCC-TTCAACTTGTGTGGGCTTTAAAAGAAAAAA-AAAGTGTTCTACTCT
129 TGAGGACTAAAAG-TGCCACT-AGCTTATGT-GGCTTTAAAAGAAAAAAGAAAGTGTCCTACTCT
*
123325 TTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCC
191 TTGAGGACTAAAAGGTGCCACCAACTTGTATGGGCTTTGAAAGGAAAAGGCATCC
* * * *
123380 TACTCTTTAAAGACTAAAAGGTGTCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCTTACT
1 TACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCATACT
* * * * * *
123445 TTTTAAAGATTAAAGGTGCCACCAGCTTGTGTGGCCTTTAAAAGAAAAAAGAATCTTACTCTTTG
66 TTTTGAAGATAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAAGAATCATGCTCTTTG
*
123510 AGGACTAAAAAGTGCCACTAGCTTATGTAGGCTTTAAAAGAAAAAAGAAAGTGTCCTACTTTTTG
131 AGGACT-AAAAGTGCCACTAGCTTATGT-GGCTTTAAAAGAAAAAAGAAAGTGTCCTACTCTTTG
** * * * *
123575 AGGACTAAAATATGCCACCAATTTGTATAGGCTTTGAAAGAAAAAGGCATCA
194 AGGACTAAAAGGTGCCACCAACTTGTATGGGCTTTGAAAGGAAAAGGCATCC
* * * *
123627 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGACTTTGAAAA-GAAAAGGCATCCTAC
1 TACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCGTCATAC
* * * * * *
123691 TCTTTGAGGAATAAAAGGTGCCACCAACTTGTATGGGCTTTAAAA-AGAAAAGGTATCCTGCTCT
65 TTTTTGAAG-ATAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA-AAAAAGAATCATGCTCT
* * * * * *
123755 TTGAAGACTAAAGGTGCCACCAGCTTATATGAGCTTTAAAA-AGAAAAAG-AA---TCTTGCTCT
128 TTGAGGACTAAAAGTGCCACTAGCTTATGTG-GCTTTAAAAGA-AAAAAGAAAGTGTCCTACTCT
* * * * * ***
123815 TTGAGGATTAAAAGGTGTCACCAGCTTGTTTGGGCTTTAAAAGGAAAAGATGTCC
191 TTGAGGACTAAAAGGTGCCACCAACTTGTATGGGCTTTGAAAGGAAAAGGCATCC
* *
123870 TGCTCTTTGAGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAAA
1 TACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
123924 TGCATCCTTC
Statistics
Matches: 460, Mismatches: 74, Indels: 24
0.82 0.13 0.04
Matches are distributed among these distances:
242 4 0.01
243 94 0.20
246 83 0.18
247 221 0.48
248 58 0.13
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (245 bp):
TACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCATACT
TTTTGAAGATAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAAGAATCATGCTCTTTG
AGGACTAAAAGTGCCACTAGCTTATGTGGCTTTAAAAGAAAAAAGAAAGTGTCCTACTCTTTGAG
GACTAAAAGGTGCCACCAACTTGTATGGGCTTTGAAAGGAAAAGGCATCC
Found at i:123687 original size:308 final size:304
Alignment explanation
Indices: 123133--123969 Score: 851
Period size: 308 Copynumber: 2.7 Consensus size: 304
123123 GAAAGTGTCT
* * * * * ** * **
123133 TACTCTTTGAGGACTAAAAGGTGTCACCAACTTATATGGGCTTT-AAAAGAAAAAGGCGTCATGT
1 TACTCTTTAAAGACT-AAAGGTGCCACCAGCTTATATGAGCTTTAAAAAGAAAAA-GAATCTTAC
* * * * * * * * * *
123197 TCTTTGATGACTAAAAGGTGTCACCAACTTGTGTGGGCTTTAAAAG-GAAA-ATGCATCATGCTT
64 TCTTTGAGGACTAAAAAGTGCCACCAGCTTATGTAGGCTTTAAAAGAAAAAGATG--TCCTACTC
* * ** * * * *
123260 TTTGAGGGCTAAAAGTTGCCTTCAACTTGTGTGGGCTTTAAAAGAAAAAAAAAGTG-TTC-TACT
127 TTTGAGGACTAAAAGATGCCACCAACTTGTATAGGCTTTAAAAG----AAAAAG-GCATCATGCT
* *
123323 CTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCATCCTACTCTTT
187 CTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGACTTTGAAAAGAAAAGGCATCCTACTCTTT
* * * * * *
123388 AAAGACTAAAAGGTGTCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCT
252 AAAGAATAAAAGGTGCCACCAACTTGTATGGGCTTTAAAAAGAAAAGGCATCC
* * * *
123441 TACTTTTTAAAGATTAAAGGTGCCACCAGCTTGTGTG-GCCTTT-AAAAGAAAAAAGAATCTTAC
1 TACTCTTTAAAGACTAAAGGTGCCACCAGCTTATATGAG-CTTTAAAAAG-AAAAAGAATCTTAC
*
123504 TCTTTGAGGACTAAAAAGTGCCACTAGCTTATGTAGGCTTTAAAAGAAAAAAGAAAGTGTCCTAC
64 TCTTTGAGGACTAAAAAGTGCCACCAGCTTATGTAGGCTTTAAAAG-AAAAAG--A-TGTCCTAC
* * * *
123569 TTTTTGAGGACTAAAATATGCCACCAATTTGTATAGGCTTTGAAAGAAAAAGGCATCATGCTCTT
125 TCTTTGAGGACTAAAAGATGCCACCAACTTGTATAGGCTTTAAAAGAAAAAGGCATCATGCTCTT
* *
123634 TGAGGACTAAAAGGTGCCACCAACTTGTGTGGACTTTGAAAAGAAAAGGCATCCTACTCTTTGAG
190 TGAGGACTAAAAGGTGCCACCAACTTGTGTGGACTTTGAAAAGAAAAGGCATCCTACTCTTTAAA
*
123699 GAATAAAAGGTGCCACCAACTTGTATGGGCTTTAAAAAGAAAAGGTATCC
255 GAATAAAAGGTGCCACCAACTTGTATGGGCTTTAAAAAGAAAAGGCATCC
* * *
123749 TGCTCTTTGAAGACTAAAGGTGCCACCAGCTTATATGAGCTTTAAAAAGAAAAAGAATCTTGCTC
1 TACTCTTTAAAGACTAAAGGTGCCACCAGCTTATATGAGCTTTAAAAAGAAAAAGAATCTTACTC
* * * * * * * *
123814 TTTGAGGATTAAAAGGTGTCACCAGCTTGTTTGGGCTTTAAAAGGAAAAGATGTCCTGCTCTTTG
66 TTTGAGGACTAAAAAGTGCCACCAGCTTATGTAGGCTTTAAAAGAAAAAGATGTCCTACTCTTTG
* * * * * * * *
123879 AGGACTAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAAATGCATCCTTCTCTTTGAGGA
131 AGGACTAAAAGATGCCACCAACTTGTATAGGCTTTAAAAGAAAAAGGCATCATGCTCTTTGAGGA
* * * *
123944 CAAAAATGTACCACCAGCTTGTGTGG
196 CTAAAAGGTGCCACCAACTTGTGTGG
123970 GGTTTAAGAG
Statistics
Matches: 440, Mismatches: 77, Indels: 28
0.81 0.14 0.05
Matches are distributed among these distances:
304 88 0.20
305 1 0.00
306 2 0.00
307 83 0.19
308 213 0.48
309 9 0.02
311 41 0.09
312 1 0.00
313 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.28
Consensus pattern (304 bp):
TACTCTTTAAAGACTAAAGGTGCCACCAGCTTATATGAGCTTTAAAAAGAAAAAGAATCTTACTC
TTTGAGGACTAAAAAGTGCCACCAGCTTATGTAGGCTTTAAAAGAAAAAGATGTCCTACTCTTTG
AGGACTAAAAGATGCCACCAACTTGTATAGGCTTTAAAAGAAAAAGGCATCATGCTCTTTGAGGA
CTAAAAGGTGCCACCAACTTGTGTGGACTTTGAAAAGAAAAGGCATCCTACTCTTTAAAGAATAA
AAGGTGCCACCAACTTGTATGGGCTTTAAAAAGAAAAGGCATCC
Found at i:124269 original size:123 final size:123
Alignment explanation
Indices: 124029--124395 Score: 519
Period size: 123 Copynumber: 3.0 Consensus size: 123
124019 AAAGGAAAGT
*
124029 GTCCTGCTCTTTAAGGACTAAAAGGTGCCA-TGAACTTGTGTAGGCTTTAAAAGG-AAAAGGCGT
1 GTCCTGCTCTTTAAGGACTAAAAGGTGCCACT-AACTTGTGTGGGCTTT-AAAGGAAAAAGGCGT
* * * *
124092 CATGCTCTTTAAGGACTAAAAGATGCCACCAATTTGTGTGGGCCTTAAAAAGAAAAA-AC
64 CATGCTCTTTAAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGAC
* * **
124151 GTCCTACTCTTTGAA-GACTAAAAGGTGCCACTAGCTTGTGTGGGCTTTAGAAGGAAAAATACGT
1 GTCCTGCTCTTT-AAGGACTAAAAGGTGCCACTAACTTGTGTGGGCTTTA-AAGGAAAAAGGCGT
*
124215 CTTGCTCTTTAAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAAGAC
64 CATGCTCTTTAAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAG-AAAAAGAC
* * *
124276 GTCCTGCTCTTTAAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAA-GAAAAAGGCATCA
1 GTCCTGCTCTTTAAGGACTAAAAGGTGCCACTAACTTGTGTGGGCTTTAAAGGAAAAAGGCGTCA
* *
124340 TGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTAGGCTTTAAAAAGAAAAAG
66 TGCTCTTTAAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAG
124396 GCATCCTATT
Statistics
Matches: 218, Mismatches: 20, Indels: 14
0.87 0.08 0.06
Matches are distributed among these distances:
121 1 0.00
122 50 0.23
123 114 0.52
124 9 0.04
125 44 0.20
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.25
Consensus pattern (123 bp):
GTCCTGCTCTTTAAGGACTAAAAGGTGCCACTAACTTGTGTGGGCTTTAAAGGAAAAAGGCGTCA
TGCTCTTTAAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGAC
Found at i:124303 original size:63 final size:61
Alignment explanation
Indices: 124004--124395 Score: 457
Period size: 61 Copynumber: 6.3 Consensus size: 61
123994 CTAGTTTGTA
* ** *
124004 TGGGCTTTAAAAGAAAAAGGAAAGTGTCCTGCTCTTTAAGGACTAAAAGGTGCCATGAACTTGTG
1 TGGGCTTTAAAAGAAAAA-G--A-CGTCCTGCTCTTTAAGGACTAAAAGGTGCCACCAACTCGTG
* * * * * * *
124069 TAGGCTTTAAAAGGAAAAGGCGTCATGCTCTTTAAGGACTAAAAGATGCCACCAATTTGTG
1 TGGGCTTTAAAAGAAAAAGACGTCCTGCTCTTTAAGGACTAAAAGGTGCCACCAACTCGTG
* * * * *
124130 TGGGCCTTAAAAAGAAAAA-ACGTCCTACTCTTTGAA-GACTAAAAGGTGCCACTAGCTTGTG
1 TGGG-CTTTAAAAGAAAAAGACGTCCTGCTCTTT-AAGGACTAAAAGGTGCCACCAACTCGTG
* * *
124191 TGGGCTTTAGAAGGAAAAATACGTCTTGCTCTTTAAGGACTAAAAGGTGCCACCAACTCGTG
1 TGGGCTTTA-AAAGAAAAAGACGTCCTGCTCTTTAAGGACTAAAAGGTGCCACCAACTCGTG
124253 TGGGCTTTAAAAAGAAAAAAGACGTCCTGCTCTTTAAGGACTAAAAGGTGCCACCAACTCGTG
1 TGGGCTTT-AAAAG-AAAAAGACGTCCTGCTCTTTAAGGACTAAAAGGTGCCACCAACTCGTG
* * * *
124316 TGGGCTTT-AAAGAAAAAGGCATCATGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTG
1 TGGGCTTTAAAAGAAAAAGACGTCCTGCTCTTTAAGGACTAAAAGGTGCCACCAACTCGTG
*
124376 TAGGCTTTAAAAAGAAAAAG
1 TGGGCTTT-AAAAGAAAAAG
124396 GCATCCTATT
Statistics
Matches: 284, Mismatches: 34, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
60 55 0.19
61 88 0.31
62 69 0.24
63 55 0.19
64 1 0.00
65 16 0.06
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (61 bp):
TGGGCTTTAAAAGAAAAAGACGTCCTGCTCTTTAAGGACTAAAAGGTGCCACCAACTCGTG
Found at i:124511 original size:32 final size:32
Alignment explanation
Indices: 124440--124522 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 32
124430 GGGTGCCACA
* *
124440 GAGTCGTGGATTTTG-AG--AGAGATGTCACT
1 GAGTCGTGGACTTTGAAGAAAGAAATGTCACT
* *
124469 AAGTCATGGACTTTGAAGAAAGAAATGTCACT
1 GAGTCGTGGACTTTGAAGAAAGAAATGTCACT
*
124501 GAGTCGTGGACTTTGAAAAAAG
1 GAGTCGTGGACTTTGAAGAAAG
124523 GTTGCTTTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 12 0.27
30 2 0.05
32 30 0.68
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.27
Consensus pattern (32 bp):
GAGTCGTGGACTTTGAAGAAAGAAATGTCACT
Found at i:125691 original size:15 final size:15
Alignment explanation
Indices: 125671--125717 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
125661 CCTTTTCTCT
125671 TTTTTTGCTTTTTTG
1 TTTTTTGCTTTTTTG
125686 TTTTTTGCTTTTTCT-
1 TTTTTTGCTTTTT-TG
*
125701 TTTTTT-CATTTTTG
1 TTTTTTGCTTTTTTG
125715 TTT
1 TTT
125718 ATCTTATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 1 0.03
14 8 0.28
15 19 0.66
16 1 0.03
ACGTcount: A:0.02, C:0.09, G:0.09, T:0.81
Consensus pattern (15 bp):
TTTTTTGCTTTTTTG
Found at i:130582 original size:79 final size:78
Alignment explanation
Indices: 130498--130648 Score: 214
Period size: 79 Copynumber: 1.9 Consensus size: 78
130488 TCTCGATTAA
* * * *
130498 AAAAATTAATATTTTGAAAATAAAA-AAGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGA
1 AAAAATCAATATTTTGAAAATAAAACAA--GGTTGGAATATCCCCTCAAAAATAACGGGATTGGA
*
130562 GTATCCCCGATAGTG
64 ATATCCCCGATAGTG
*
130577 AAAAATCAATCTTTTGAAAATAAAATCAAGGTTGGAATATCCCCTCAAAAATAACGGGATTGGAA
1 AAAAATCAATATTTTGAAAATAAAA-CAAGGTTGGAATATCCCCTCAAAAATAACGGGATTGGAA
130642 TATCCCC
65 TATCCCC
130649 TCGGAAGTAA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
79 62 0.97
81 2 0.03
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.25
Consensus pattern (78 bp):
AAAAATCAATATTTTGAAAATAAAACAAGGTTGGAATATCCCCTCAAAAATAACGGGATTGGAAT
ATCCCCGATAGTG
Found at i:130758 original size:76 final size:74
Alignment explanation
Indices: 130636--131093 Score: 402
Period size: 76 Copynumber: 6.1 Consensus size: 74
130626 AATAACGGGA
* * * * * *
130636 TTGGAATATCCCCTCG-GAAGTAATGAAGTTAGAGTATCCCTGATAAAAATCGACATTTTTAGAA
1 TTGGAGTATCCCCTCGAGAAATAATG-GGTTGGAGTATCCC-AATAAAAATCAACATTTTTAGAA
130700 GTAAAAATGAGG
64 GTAAAAA-GAGG
** * * *
130712 TTGGAGTATTTCTTCGA-AAATAATAGGGTTGGAGTACTCCCAATAAAAATCAAAATTTTTAAAA
1 TTGGAGTATCCCCTCGAGAAATAAT-GGGTTGGAGTA-TCCCAATAAAAATCAACATTTTTAGAA
*
130776 GT-AAAA-ACG
64 GTAAAAAGAGG
* * * *
130785 --GG-GT-TCCCTTCGA-AAATAATGGGGTTAGAGTATCTCCAATAAAAATTAGCATTTTTAGAA
1 TTGGAGTATCCCCTCGAGAAATAAT-GGGTTGGAGTATC-CCAATAAAAATCAACATTTTTAGAA
*
130845 GTAAAAACAGGG
64 GTAAAAAGA-GG
* *
130857 TTGGAGTATCCCCTC-AGAAATAATGAGGTTGGAGTACTCCTAATAAAAATCGACATTTTTAGAA
1 TTGGAGTATCCCCTCGAGAAATAATG-GGTTGGAGTA-TCCCAATAAAAATCAACATTTTTAGAA
*
130921 GTAAAAATGTGG
64 GTAAAAA-GAGG
* * * **
130933 TTAGAGTATCTCCTCGA-AAATAATAGGGTTAGAGTATCCTTGAT-AAAATCAACATTTTTAGAA
1 TTGGAGTATCCCCTCGAGAAATAAT-GGGTTGGAGTATCC-CAATAAAAATCAACATTTTTAGAA
130996 GTAAAAACGAGG
64 GTAAAAA-GAGG
* ** *
131008 TTGGAGTATCCCCTC-AGAAATGATGGGATTGGAGTATCCCCGGTAAAAATCAACATTTTTAGAG
1 TTGGAGTATCCCCTCGAGAAATAATGGG-TTGGAGTAT-CCCAATAAAAATCAACATTTTTAGAA
*
131072 GTAAAAACGGGG
64 GTAAAAA-GAGG
131084 TTGGAGTATC
1 TTGGAGTATC
131094 TTCGATAAAT
Statistics
Matches: 316, Mismatches: 44, Indels: 44
0.78 0.11 0.11
Matches are distributed among these distances:
68 2 0.01
69 47 0.15
70 6 0.02
71 3 0.01
72 1 0.00
73 2 0.01
74 6 0.02
75 68 0.22
76 172 0.54
77 9 0.03
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (74 bp):
TTGGAGTATCCCCTCGAGAAATAATGGGTTGGAGTATCCCAATAAAAATCAACATTTTTAGAAGT
AAAAAGAGG
Found at i:130839 original size:69 final size:69
Alignment explanation
Indices: 130723--130858 Score: 193
Period size: 69 Copynumber: 2.0 Consensus size: 69
130713 TGGAGTATTT
* *
130723 CTTCGAAAATAATAGGGTTGGAGTACTCCCAATAAAAATCAAAATTTTTAAAAGTAAAAACGGGG
1 CTTCGAAAATAATAGGGTTAGAGTACTCCCAATAAAAATCAAAATTTTTAAAAGTAAAAACAGGG
130788 TTCC
66 TTCC
* * ** *
130792 CTTCGAAAATAATGGGGTTAGAGTA-TCTCCAATAAAAATTAGCATTTTTAGAAGTAAAAACAGG
1 CTTCGAAAATAATAGGGTTAGAGTACTC-CCAATAAAAATCAAAATTTTTAAAAGTAAAAACAGG
130856 GTT
65 GTT
130859 GGAGTATCCC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 2 0.03
69 57 0.97
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.28
Consensus pattern (69 bp):
CTTCGAAAATAATAGGGTTAGAGTACTCCCAATAAAAATCAAAATTTTTAAAAGTAAAAACAGGG
TTCC
Found at i:130923 original size:145 final size:144
Alignment explanation
Indices: 130663--131085 Score: 466
Period size: 145 Copynumber: 2.9 Consensus size: 144
130653 AAGTAATGAA
* * ** *
130663 GTTAGAGTATCCCTGATAAAAA-TCGACATTTTTAGAAGTAAAAATGAGGTTGGAGTATTTCTTC
1 GTTAGAGTATCCC-GATAAAAATTAG-CATTTTTAGAAGTAAAAACGAGGTTGGAGTATCCCCTC
* *
130727 -GAAAATAAT-AGGGTTGGAGTACTCCCAATAAAAATCAAAATTTTTAAAAGTAAAAACGGGGTT
64 AG-AAATAATGA-GGTTGGAGTACTCCCAATAAAAATCAACATTTTTAGAAGTAAAAACGGGGTT
*
130790 C-CCTTCGAAAATAATGGG
127 CTCC-TCGAAAATAATAGG
*
130808 GTTAGAGTATCTCCAATAAAAATTAGCATTTTTAGAAGTAAAAAC-AGGGTTGGAGTATCCCCTC
1 GTTAGAGTATC-CCGATAAAAATTAGCATTTTTAGAAGTAAAAACGA-GGTTGGAGTATCCCCTC
* * *
130872 AGAAATAATGAGGTTGGAGTACTCCTAATAAAAATCGACATTTTTAGAAGTAAAAATGTGGTTAG
64 AGAAATAATGAGGTTGGAGTACTCCCAATAAAAATCAACATTTTTAGAAGTAAAAA--CGG---G
130937 AGTATCTCCTCGAAAATAATAGG
124 -GT-TCTCCTCGAAAATAATAGG
* * *
130960 GTTAGAGTATCCTTGAT-AAAATCAACATTTTTAGAAGTAAAAACGAGGTTGGAGTATCCCCTCA
1 GTTAGAGTATCC-CGATAAAAATTAGCATTTTTAGAAGTAAAAACGAGGTTGGAGTATCCCCTCA
* ** *
131024 GAAATGATG-GGATTGGAGTA-TCCCCGGTAAAAATCAACATTTTTAGAGGTAAAAACGGGGTT
65 GAAATAATGAGG-TTGGAGTACT-CCCAATAAAAATCAACATTTTTAGAAGTAAAAACGGGGTT
131086 GGAGTATCTT
Statistics
Matches: 238, Mismatches: 23, Indels: 35
0.80 0.08 0.12
Matches are distributed among these distances:
144 2 0.01
145 100 0.42
146 7 0.03
147 2 0.01
149 2 0.01
150 4 0.02
151 90 0.38
152 29 0.12
153 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.29
Consensus pattern (144 bp):
GTTAGAGTATCCCGATAAAAATTAGCATTTTTAGAAGTAAAAACGAGGTTGGAGTATCCCCTCAG
AAATAATGAGGTTGGAGTACTCCCAATAAAAATCAACATTTTTAGAAGTAAAAACGGGGTTCTCC
TCGAAAATAATAGG
Found at i:131023 original size:151 final size:151
Alignment explanation
Indices: 130663--131094 Score: 487
Period size: 151 Copynumber: 2.9 Consensus size: 151
130653 AAGTAATGAA
* * * ** *
130663 GTTAGAGTATCCCTGATAAAAATCGACATTTTTAGAAGTAAAAATGAGGTTGGAGTATTTCTTC-
1 GTTAGAGTATCCTTGATAAAAATCAACATTTTTAGAAGTAAAAACGAGGTTGGAGTATCCCCTCA
* *
130727 GAAAATAAT-AGGGTTGGAGTACTCCCAATAAAAATCAAAATTTTTAAAAGTAAAAA-CGG--G-
66 G-AAATAATGA-GGTTGGAGTACTCCCAATAAAAATCAACATTTTTAGAAGTAAAAAGCGGTTGA
*
130787 GT-TC-CCTTCGAAAATAATGGG
129 GTATCTCCTTCGAAAATAATAGG
** * *
130808 GTTAGAGTAT-CTCCAATAAAAATTAGCATTTTTAGAAGTAAAAAC-AGGGTTGGAGTATCCCCT
1 GTTAGAGTATCCT-TGATAAAAATCAACATTTTTAGAAGTAAAAACGA-GGTTGGAGTATCCCCT
* * *
130871 CAGAAATAATGAGGTTGGAGTACTCCTAATAAAAATCGACATTTTTAGAAGTAAAAATGTGGTTA
64 CAGAAATAATGAGGTTGGAGTACTCCCAATAAAAATCAACATTTTTAGAAGTAAAAA-GCGGTT-
130936 GAGTATCTCC-TCGAAAATAATAGG
127 GAGTATCTCCTTCGAAAATAATAGG
130960 GTTAGAGTATCCTTGAT-AAAATCAACATTTTTAGAAGTAAAAACGAGGTTGGAGTATCCCCTCA
1 GTTAGAGTATCCTTGATAAAAATCAACATTTTTAGAAGTAAAAACGAGGTTGGAGTATCCCCTCA
* ** * *
131024 GAAATGATG-GGATTGGAGTA-TCCCCGGTAAAAATCAACATTTTTAGAGGTAAAAACGGGGTTG
66 GAAATAATGAGG-TTGGAGTACT-CCCAATAAAAATCAACATTTTTAGAAGTAAAAA-GCGGTT-
131087 GAGTATCT
127 GAGTATCT
131095 TCGATAAATA
Statistics
Matches: 242, Mismatches: 29, Indels: 26
0.81 0.10 0.09
Matches are distributed among these distances:
144 2 0.01
145 98 0.40
146 2 0.01
147 2 0.01
150 4 0.02
151 102 0.42
152 28 0.12
153 4 0.02
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (151 bp):
GTTAGAGTATCCTTGATAAAAATCAACATTTTTAGAAGTAAAAACGAGGTTGGAGTATCCCCTCA
GAAATAATGAGGTTGGAGTACTCCCAATAAAAATCAACATTTTTAGAAGTAAAAAGCGGTTGAGT
ATCTCCTTCGAAAATAATAGG
Found at i:132650 original size:21 final size:21
Alignment explanation
Indices: 132624--132679 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
132614 AGGGTGGTTT
132624 TGTATCGATACATTTTAGGCA
1 TGTATCGATACATTTTAGGCA
132645 TGTATCGATACATTTTAGGCA
1 TGTATCGATACATTTTAGGCA
132666 TGTATCGATACATT
1 TGTATCGATACATT
132680 CACTTATGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (21 bp):
TGTATCGATACATTTTAGGCA
Found at i:132690 original size:20 final size:21
Alignment explanation
Indices: 132665--132718 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
132655 CATTTTAGGC
132665 ATGTATCGATACATTCACT-T
1 ATGTATCGATACATTCACTAT
* *
132685 ATGTATCTATACATTTACTAT
1 ATGTATCGATACATTCACTAT
*
132706 TTGTATCGATACA
1 ATGTATCGATACA
132719 AATTGTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTCACTAT
Found at i:134033 original size:13 final size:13
Alignment explanation
Indices: 134003--134076 Score: 55
Period size: 13 Copynumber: 5.5 Consensus size: 13
133993 ATTTTATATA
*
134003 ATTAAATTTTAATT
1 ATTAAA-TTTATTT
134017 -TTAAATTTATTT
1 ATTAAATTTATTT
134029 ATTAAATATT-TTT
1 ATTAAAT-TTATTT
*
134042 AAATAAATTT-TATT
1 -ATTAAATTTAT-TT
134056 ATTAAATTTTATTT
1 ATTAAA-TTTATTT
134070 AATTAAA
1 -ATTAAA
134077 AATTTTATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
12 6 0.12
13 22 0.44
14 15 0.30
15 7 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTAAATTTATTT
Found at i:134048 original size:27 final size:28
Alignment explanation
Indices: 134018--134092 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 28
134008 ATTTTAATTT
134018 TAAA-TTTATTTATTAAATATT-TTTAAA
1 TAAATTTTA-TTATTAAATATTATTTAAA
* *
134045 TAAATTTTATTATTAAATTTTATTTAAT
1 TAAATTTTATTATTAAATATTATTTAAA
**
134073 TAAAAATT-TTA-TAAATATTA
1 TAAATTTTATTATTAAATATTA
134093 AAACTCCTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
26 8 0.20
27 18 0.44
28 15 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TAAATTTTATTATTAAATATTATTTAAA
Found at i:134073 original size:23 final size:23
Alignment explanation
Indices: 133988--134073 Score: 57
Period size: 27 Copynumber: 3.3 Consensus size: 23
133978 CTTAACTTAT
133988 TTTATATTTTATATAATTAAATTTTAA
1 TTTA-ATTTTAT-T-ATTAAATTTT-A
*
134015 TTTTAAATTTATTTATTAAATATTT-
1 -TTTAATTTTA-TTATTAAAT-TTTA
134040 TTAAATAAATTTTATTATTAAATTTTA
1 TT---T-AATTTTATTATTAAATTTTA
134067 TTTAATT
1 TTTAATT
134074 AAAAATTTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 19
0.70 0.03 0.27
Matches are distributed among these distances:
23 4 0.08
24 3 0.06
26 10 0.20
27 21 0.43
28 11 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTAATTTTATTATTAAATTTTA
Found at i:136168 original size:80 final size:80
Alignment explanation
Indices: 135761--136170 Score: 314
Period size: 80 Copynumber: 5.2 Consensus size: 80
135751 CTCGAAGCTT
* * ** * * *
135761 GTGGGGTTGGAGTTTCCCTAGAGATGTAAAATTTGATGTTCT-GAAAGTAAAAACGGGGTTGGAG
1 GTGGGGTTGGAGTATCCCTAGAGATGAAAAATTCAATATTTTAG-AAGTAAAAATGGGGTTGGAG
*
135825 TAT-CCC-TCGAAAATG
65 TATCCCCTTAG-AAATG
* * * * * ** *
135840 GTGGGGTTAGAGTATCCCT-GAGATGAAAATTTTAGTGTTTTAGAAGTAAAAATGTAGTTGAAGT
1 GTGGGGTTGGAGTATCCCTAGAGATGAAAAATTCAATATTTTAGAAGTAAAAATGGGGTTGGAGT
* * *
135904 ATCTCCTAAAAAAATG
66 ATCCCCT-TAGAAATG
* * * * *
135920 GTGGGGTTGGAGGATCCCTAAAGGTGAAGAAATTCAATATTTTAGAAGTAAAAATAGGATTGGAG
1 GTGGGGTTGGAGTATCCCTAGAGATGAA-AAATTCAATATTTTAGAAGTAAAAATGGGGTTGGAG
*
135985 TAT-CCC-TAAATAATG
65 TATCCCCTTAGA-AATG
* * * * * *
136000 ATAGGGTTGGAGTAT--CTAGAGATGAAGAAATTCAATATTTTAAAAATAAAAAAGAGGTTGGAG
1 GTGGGGTTGGAGTATCCCTAGAGATGAA-AAATTCAATATTTTAGAAGTAAAAATGGGGTTGGAG
* * * *
136063 TATCTCTTTGGAGATG
65 TATCCCCTTAGAAATG
* * * * ** *
136079 GTGGCGTTGGAGTATCCCCAAAGATGTAAAATTCGGTATTTTGGAAGTAAAAATGGGGTTGGAGT
1 GTGGGGTTGGAGTATCCCTAGAGATGAAAAATTCAATATTTTAGAAGTAAAAATGGGGTTGGAGT
*
136144 ATCCCCTTAGAAATT
66 ATCCCCTTAGAAATG
*
136159 GTGAGGTTGGAG
1 GTGGGGTTGGAG
136171 ATGGGATTGG
Statistics
Matches: 254, Mismatches: 66, Indels: 21
0.74 0.19 0.06
Matches are distributed among these distances:
78 79 0.31
79 39 0.15
80 90 0.35
81 16 0.06
82 30 0.12
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.30
Consensus pattern (80 bp):
GTGGGGTTGGAGTATCCCTAGAGATGAAAAATTCAATATTTTAGAAGTAAAAATGGGGTTGGAGT
ATCCCCTTAGAAATG
Found at i:136276 original size:120 final size:120
Alignment explanation
Indices: 136057--136290 Score: 299
Period size: 120 Copynumber: 1.9 Consensus size: 120
136047 AAAAAAGAGG
* * * * * **
136057 TTGGAGTATCTCTTTGGAGATGGTGGCGTTGGAGTATCCCCAAAGATGTAAAATTCGGTATTTTG
1 TTGGAGTATCTCTTCGAAAATGGTGGCGTTGAAGTATCCCCAAAGATGAAAAATTCAATATTTTG
* * * *
136122 GAAGTAAAAATGGGGTTGGAGTATCCCCTTAGAAATTGTGAGGTTGGAGATGGGA
66 GAAGTAAAAACGGGGTTAGAGTATACCCTTAGAAATTATGAGGTTGGAGATGGGA
* * * * *
136177 TTGGAGTATCTCTTCGAAAATGGTGGGGTTGAAGTATCTCTAGAGATGAAAAATTCAATCTTTTG
1 TTGGAGTATCTCTTCGAAAATGGTGGCGTTGAAGTATCCCCAAAGATGAAAAATTCAATATTTTG
*
136242 GAAGTAAAAACGGGGTTAGAGTA-ACCCTTCAGAAATTATGGGGTTGGAG
66 GAAGTAAAAACGGGGTTAGAGTATACCCTT-AGAAATTATGAGGTTGGAG
136291 TATTCCCGGA
Statistics
Matches: 96, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
119 5 0.05
120 91 0.95
ACGTcount: A:0.29, C:0.10, G:0.30, T:0.30
Consensus pattern (120 bp):
TTGGAGTATCTCTTCGAAAATGGTGGCGTTGAAGTATCCCCAAAGATGAAAAATTCAATATTTTG
GAAGTAAAAACGGGGTTAGAGTATACCCTTAGAAATTATGAGGTTGGAGATGGGA
Found at i:137319 original size:18 final size:19
Alignment explanation
Indices: 137296--137336 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
137286 ACCAAGGCTT
137296 AAAATACTTATTAAG-TAA
1 AAAATACTTATTAAGTTAA
* *
137314 AAAATATTTTTTAAGTTAA
1 AAAATACTTATTAAGTTAA
137333 AAAA
1 AAAA
137337 CAGCATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (19 bp):
AAAATACTTATTAAGTTAA
Found at i:138927 original size:20 final size:21
Alignment explanation
Indices: 138902--138956 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
138892 CATTACAAGC
*
138902 ATGTATCGATACATTCA-CTT
1 ATGTATCGATACAATCAGCTT
138922 ATGTATCGATA-AATCAGCTT
1 ATGTATCGATACAATCAGCTT
*
138942 ATTATATCGATACAA
1 A-TGTATCGATACAA
138957 ATTGTAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.13
20 15 0.50
21 9 0.30
22 2 0.07
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (21 bp):
ATGTATCGATACAATCAGCTT
Found at i:139191 original size:36 final size:36
Alignment explanation
Indices: 139141--139212 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
139131 TCTAAAAGTA
139141 TTTTTATTCATTTACATATATATATATATATATATC
1 TTTTTATTCATTTACATATATATATATATATATATC
**
139177 TTTTTATTTGTTTACATATATATATATATATATATC
1 TTTTTATTCATTTACATATATATATATATATATATC
139213 CTTTCGATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.57
Consensus pattern (36 bp):
TTTTTATTCATTTACATATATATATATATATATATC
Found at i:139451 original size:70 final size:71
Alignment explanation
Indices: 139362--139694 Score: 318
Period size: 70 Copynumber: 4.7 Consensus size: 71
139352 AGACTTTGAG
* * * * * *
139362 AAAG-AAAAAGAGTCTTACTCTTTGCGGA-TAAAAGGGATAAAGGGTGCCACTAGCTTGTATGGG
1 AAAGAAAAAAGCGTCCTACTCTTTGAGGACTAAAAAGGATAAAAGGTGCCACTAGCTTGTATGAG
139425 CTTTAA
66 CTTTAA
* * * * *
139431 AATGAAAAAGGCATCCTACTCTTTGAGGACT-GAAAGGATAAAAGGTGCCACCAGCTTGTATGAG
1 AAAGAAAAAAGCGTCCTACTCTTTGAGGACTAAAAAGGATAAAAGGTGCCACTAGCTTGTATGAG
139495 CTTTAA
66 CTTTAA
* * * *
139501 AAAGGAAAAAAAGCGTCCTACTCTTTAAGGACTAAAAAAGATAAAAGGGTGTCA-TCAGCTTGTG
1 AAA-G-AAAAAAGCGTCCTACTCTTTGAGGACTAAAAAGGATAAAA-GGTGCCACT-AGCTTGTA
139565 TGAGCTTTAA
62 TGAGCTTTAA
* * * * * * *
139575 AAAGAAAAAATCGTCTTACTCTTTGATGATTAAAAAGGATAAAAGGTGCCACCA-ATTTTATGAG
1 AAAGAAAAAAGCGTCCTACTCTTTGAGGACTAAAAAGGATAAAAGGTGCCACTAGCTTGTATGAG
139639 CTTT-A
66 CTTTAA
* * * * * * * *
139644 AAAGCAAAAAGCATCTTGCTCTTCGAAGACTAAAAAAGATAAAATGTGCCA
1 AAAGAAAAAAGCGTCCTACTCTTTGAGGACTAAAAAGGATAAAAGGTGCCA
139695 TCAACTTATG
Statistics
Matches: 216, Mismatches: 40, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
69 46 0.21
70 66 0.31
71 9 0.04
72 58 0.27
73 11 0.05
74 26 0.12
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (71 bp):
AAAGAAAAAAGCGTCCTACTCTTTGAGGACTAAAAAGGATAAAAGGTGCCACTAGCTTGTATGAG
CTTTAA
Found at i:139562 original size:144 final size:141
Alignment explanation
Indices: 139336--139687 Score: 349
Period size: 144 Copynumber: 2.5 Consensus size: 141
139326 AGTAGATAAA
* * ** **
139336 TGCCACCAACTTATAT-AGACTTTGAGAAAG-AAAAAGAGTCTTACTCTTTGCGGA-TAAAAGGG
1 TGCCACCAA-TTGTATGAG-CTTT-A-AAAGAAAAAAGCGTCTTACTCTTTAAGGACTAAAAAAG
* * *
139398 AT-AAAGGGTGCCACTAGCTTGTATGGGCTTTAAAATGAAAAAGGCATCCTACTCTTTGAGGACT
62 ATAAAAGGGTGCCACTAGCTTGTATGAGCTTTAAAAAGAAAAAAGCATCCTACTCTTTGAGGACT
*
139462 -GAAAGGATAAAAGG
127 AAAAAGGATAAAAGG
* *
139476 TGCCACCAGCTTGTATGAGCTTTAAAAAGGAAAAAAAGCGTCCTACTCTTTAAGGACTAAAAAAG
1 TGCCACCA-ATTGTATGAGCTTT-AAAA-G-AAAAAAGCGTCTTACTCTTTAAGGACTAAAAAAG
* * * * * * *
139541 ATAAAAGGGTGTCA-TCAGCTTGTGTGAGCTTTAAAAAGAAAAAATCGTCTTACTCTTTGATGAT
62 ATAAAAGGGTGCCACT-AGCTTGTATGAGCTTTAAAAAGAAAAAAGCATCCTACTCTTTGAGGAC
139605 TAAAAAGGATAAAAGG
126 TAAAAAGGATAAAAGG
* * * * *
139621 TGCCACCAATTTTATGAGCTTTAAAAGCAAAAAGCATCTTGCTCTTCGAA-GACTAAAAAAGATA
1 TGCCACCAATTGTATGAGCTTTAAAAGAAAAAAGCGTCTTACTCTT-TAAGGACTAAAAAAGATA
139685 AAA
65 AAA
139688 TGTGCCATCA
Statistics
Matches: 175, Mismatches: 27, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
139 3 0.02
140 19 0.11
141 34 0.19
142 23 0.13
143 13 0.07
144 62 0.35
145 21 0.12
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (141 bp):
TGCCACCAATTGTATGAGCTTTAAAAGAAAAAAGCGTCTTACTCTTTAAGGACTAAAAAAGATAA
AAGGGTGCCACTAGCTTGTATGAGCTTTAAAAAGAAAAAAGCATCCTACTCTTTGAGGACTAAAA
AGGATAAAAGG
Found at i:139714 original size:70 final size:70
Alignment explanation
Indices: 139421--139716 Score: 193
Period size: 72 Copynumber: 4.2 Consensus size: 70
139411 CTAGCTTGTA
* * * * * * * * *
139421 TGGGCTTTAAAATGAAAAAGGCATCCTACTCTTTGAGGACT-GAAAGGATAAAAGGTGCCACCAG
1 TGGGTTTTAAAA-GAAAAAAGCATCTTACTCTTCGAAGACTAAAAAAGATAAAAGGTGCCATCAA
* *
139485 CTTGTA
65 CTTATG
* * * * * *
139491 TGAGCTTTAAAAAGGAAAAAAAGCGTCCTACTCTT-TAAGGACTAAAAAAGATAAAAGGGTGTCA
1 TG-GGTTTTAAAA-G-AAAAAAGCATCTTACTCTTCGAA-GACTAAAAAAGATAAAA-GGTGCCA
* *
139555 TCAGCTTGTG
61 TCAACTTATG
* * * * * * * * *
139565 TGAGCTTTAAAAAGAAAAAATCGTCTTACTCTTTGATGATTAAAAAGGATAAAAGGTGCCACCAA
1 TG-GGTTTTAAAAGAAAAAAGCATCTTACTCTTCGAAGACTAAAAAAGATAAAAGGTGCCATCAA
* *
139630 -TTTTA
65 CTTATG
* * * * *
139635 TGAGCTTTAAAAGCAAAAAGCATCTTGCTCTTCGAAGACTAAAAAAGATAAAATGTGCCATCAAC
1 TGGGTTTTAAAAGAAAAAAGCATCTTACTCTTCGAAGACTAAAAAAGATAAAAGGTGCCATCAAC
139700 TTATG
66 TTATG
139705 TGGGTTTTAAAA
1 TGGGTTTTAAAA
139717 AGAATTGTTC
Statistics
Matches: 177, Mismatches: 42, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
69 48 0.27
70 20 0.11
71 17 0.10
72 53 0.30
73 12 0.07
74 27 0.15
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (70 bp):
TGGGTTTTAAAAGAAAAAAGCATCTTACTCTTCGAAGACTAAAAAAGATAAAAGGTGCCATCAAC
TTATG
Found at i:139847 original size:130 final size:130
Alignment explanation
Indices: 139594--139846 Score: 314
Period size: 130 Copynumber: 1.9 Consensus size: 130
139584 ATCGTCTTAC
* * *
139594 TCTTTGATGATTAAAAAGGATAAAAGGTGCCACCAATTTTATGAGCTTTAAAAGCAAAAAGCATC
1 TCTTTGAGGATTAAAAAGGATAAAAGGTGCCACCAATTGTATAAGCTTTAAAA-CAAAAAGCATC
* * *
139659 TTGCTCTTCGAAGACTAAAAAAGATAAAATGTGCCATCAACTTATGTGGGTTTTAAAAAGAATTG
65 TTGCTCTTCGAAGACTAAAAAAGATAAAAAGTGCCACCAACTTATGTGGATTTTAAAAAGAATTG
139724 T
130 T
* * * *
139725 TCTTTGAGGATT-AAAAGGATAAAAGGTGCCACCAGCTTGTGTAAGTTTTAAAA-AAAAAGGTAT
1 TCTTTGAGGATTAAAAAGGATAAAAGGTGCCACCA-ATTGTATAAGCTTTAAAACAAAAA-GCAT
* * * * * *
139788 CTTGCTTTTTGAAGACTGAAAAA-ATAAAAAGTGCTACCGATTTATGTGGATTTTAAAAA
64 CTTGCTCTTCGAAGACTAAAAAAGATAAAAAGTGCCACCAACTTATGTGGATTTTAAAAA
139847 AAGAAAAAAA
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
129 35 0.34
130 45 0.43
131 24 0.23
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (130 bp):
TCTTTGAGGATTAAAAAGGATAAAAGGTGCCACCAATTGTATAAGCTTTAAAACAAAAAGCATCT
TGCTCTTCGAAGACTAAAAAAGATAAAAAGTGCCACCAACTTATGTGGATTTTAAAAAGAATTGT
Found at i:143738 original size:2 final size:2
Alignment explanation
Indices: 143731--143766 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
143721 CATAGATGTG
143731 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
143767 ATTTCTTGTT
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):
TA
Found at i:144252 original size:20 final size:18
Alignment explanation
Indices: 144217--144261 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
144207 AGTATTTAAA
144217 TAATTTTTTTAATACTAT
1 TAATTTTTTTAATACTAT
*
144235 TAATATTTTTTATTTACTA-
1 TAAT-TTTTTTA-ATACTAT
144254 TAATTTTT
1 TAATTTTT
144262 AAAGTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.33
19 11 0.46
20 5 0.21
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (18 bp):
TAATTTTTTTAATACTAT
Found at i:144615 original size:2 final size:2
Alignment explanation
Indices: 144610--144646 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
144600 TATATATATA
144610 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
144647 TTTGTGTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:144819 original size:13 final size:13
Alignment explanation
Indices: 144787--144833 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
144777 TAATTTTTTT
*
144787 ATTTATTAAAATAA
1 ATTTTTTAAAAT-A
144801 ATTTTTTATAAAT-
1 ATTTTTTA-AAATA
*
144814 ATTTTTCAAAATA
1 ATTTTTTAAAATA
144827 ATTTTTT
1 ATTTTTT
144834 TTTTAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 4 0.14
13 13 0.46
14 7 0.25
15 4 0.14
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTTTTTAAAATA
Found at i:145259 original size:53 final size:51
Alignment explanation
Indices: 145174--145286 Score: 145
Period size: 53 Copynumber: 2.2 Consensus size: 51
145164 GGATGCAAAT
* *
145174 AATTAAAAAATATGTTATATTAAATAACAAATTATAATTTAAAAATAATTAAA
1 AATTAAAAAATATGATATATGAAATAACAAATTATAATTTAAAAA-AA-TAAA
*** * *
145227 AATTAAAAAATATGATATATGAAATCTTAAATTATTATTTTAAAAAATAAA
1 AATTAAAAAATATGATATATGAAATAACAAATTATAATTTAAAAAAATAAA
145278 AATTAAAAA
1 AATTAAAAA
145287 CGTTTTATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
51 13 0.25
52 2 0.04
53 38 0.72
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (51 bp):
AATTAAAAAATATGATATATGAAATAACAAATTATAATTTAAAAAAATAAA
Found at i:146551 original size:16 final size:17
Alignment explanation
Indices: 146518--146558 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
146508 TATATTAAAA
*
146518 ATAAT-TAAAATTTAAT
1 ATAATATAAAAATTAAT
146534 ATAATATAAAAATT-AT
1 ATAATATAAAAATTAAT
146550 ATAA-ATAAA
1 ATAATATAAA
146559 TTTATTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 11 0.48
17 7 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAATATAAAAATTAAT
Found at i:146568 original size:16 final size:17
Alignment explanation
Indices: 146549--146606 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 17
146539 ATAAAAATTA
146549 TATAAATAAATTTAT-T
1 TATAAATAAATTTATCT
146565 TATAAATTAAATAATTATCT
1 TATAAA-TAAAT--TTATCT
* *
146585 AATCAAATAAATTTAACT
1 TAT-AAATAAATTTATCT
146603 TATA
1 TATA
146607 TCATATTGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
16 6 0.18
17 6 0.18
18 7 0.21
19 4 0.12
20 8 0.24
21 3 0.09
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
TATAAATAAATTTATCT
Found at i:147000 original size:17 final size:19
Alignment explanation
Indices: 146975--147012 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
146965 ATCTTAAATT
*
146975 ATTACTTATTTTAA-AGTA
1 ATTACTTATTTAAATAGTA
146993 ATTA-TTATTTAAATAGTA
1 ATTACTTATTTAAATAGTA
147011 AT
1 AT
147013 ATAGTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (19 bp):
ATTACTTATTTAAATAGTA
Found at i:147257 original size:20 final size:20
Alignment explanation
Indices: 147214--147257 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
147204 TAATTAGTTT
* *
147214 ATTATTTACATAAAAAATAT
1 ATTATTTACATAAAAAAAAA
147234 ATTATTTA-ATAAATAAAAAA
1 ATTATTTACATAAA-AAAAAA
147254 ATTA
1 ATTA
147258 AATTATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTATTTACATAAAAAAAAA
Found at i:147333 original size:27 final size:29
Alignment explanation
Indices: 147289--147342 Score: 78
Period size: 26 Copynumber: 1.9 Consensus size: 29
147279 AAATAATATA
147289 ATAAAAATTATATATTTTTAA-ATTTAAAT
1 ATAAAAATTATA-ATTTTTAATATTTAAAT
147318 ATAAAAA-T-TAATTTTTAATATTTAA
1 ATAAAAATTATAATTTTTAATATTTAA
147343 TATCATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 8 0.33
27 8 0.33
28 1 0.04
29 7 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
ATAAAAATTATAATTTTTAATATTTAAAT
Found at i:147514 original size:22 final size:22
Alignment explanation
Indices: 147467--147515 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
147457 AAATATAAAT
*
147467 ATATAAATATATCAAAATTTTT
1 ATATAAATATATCAAAATTTTA
* *
147489 ATATAAATAT-TTAATATTTTAA
1 ATATAAATATATCAAAATTTT-A
147511 ATATA
1 ATATA
147516 TTTATAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATAAATATATCAAAATTTTA
Found at i:147520 original size:30 final size:30
Alignment explanation
Indices: 147459--147526 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
147449 TAAAATTTAA
*
147459 ATATAAATATATAAATATATCAAAATTTTT
1 ATATAAATATATAAATATATCAAAATATTT
* * *
147489 ATATAAATAT-TTAATATTTTAAATATATTT
1 ATATAAATATATAAATATATCAAA-ATATTT
147519 ATAATAAA
1 AT-ATAAA
147527 AATACACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 10 0.31
30 17 0.53
31 5 0.16
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (30 bp):
ATATAAATATATAAATATATCAAAATATTT
Found at i:148691 original size:12 final size:12
Alignment explanation
Indices: 148670--148722 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
148660 TCTTGGTTAC
*
148670 TATATATATATA
1 TATATTTATATA
148682 TATATTTATATA
1 TATATTTATATA
* *
148694 TGTATTTGTATA
1 TATATTTATATA
* * *
148706 TGTATGTATGTA
1 TATATTTATATA
148718 TATAT
1 TATAT
148723 GTAGATGGCA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (12 bp):
TATATTTATATA
Found at i:148723 original size:8 final size:8
Alignment explanation
Indices: 148672--148725 Score: 53
Period size: 8 Copynumber: 7.2 Consensus size: 8
148662 TTGGTTACTA
*
148672 TATATATA
1 TATATATG
*
148680 TATATATT
1 TATATATG
148688 TATATATG
1 TATATATG
148696 TAT-T-TG
1 TATATATG
148702 --TATATG
1 TATATATG
*
148708 TATGTATG
1 TATATATG
148716 TATATATG
1 TATATATG
148724 TA
1 TA
148726 GATGGCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 1 0.03
5 1 0.03
6 4 0.11
7 1 0.03
8 31 0.82
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (8 bp):
TATATATG
Found at i:149374 original size:36 final size:36
Alignment explanation
Indices: 149320--149397 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
149310 TGGGTTATAT
*
149320 TAGATCATCTGGCGCATCATATGCCTTGCATTCAAG
1 TAGATTATCTGGCGCATCATATGCCTTGCATTCAAG
* * *
149356 TAGATTATGTGGCTCATCATATGCCTTGCATTCAAT
1 TAGATTATCTGGCGCATCATATGCCTTGCATTCAAG
149392 TAGATT
1 TAGATT
149398 TTTATTCTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (36 bp):
TAGATTATCTGGCGCATCATATGCCTTGCATTCAAG
Found at i:154004 original size:26 final size:26
Alignment explanation
Indices: 153975--154027 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
153965 CTCCAAAGCA
*
153975 AGAGGAGTTCAGCAAAGAAAAGATTG
1 AGAGGAGTTAAGCAAAGAAAAGATTG
*
154001 AGAGGAGTTAAGCAAAGAAGAGATTG
1 AGAGGAGTTAAGCAAAGAAAAGATTG
154027 A
1 A
154028 AAAGCTGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.47, C:0.06, G:0.32, T:0.15
Consensus pattern (26 bp):
AGAGGAGTTAAGCAAAGAAAAGATTG
Found at i:154418 original size:103 final size:102
Alignment explanation
Indices: 154296--154587 Score: 307
Period size: 103 Copynumber: 2.9 Consensus size: 102
154286 TGACATATAA
*
154296 ATGATTTTTGGGGATTTTATTTTATTTTTCCTTATTGTAAATCTAAAAGGATTTTTGAGATTTTT
1 ATGATTTTTGGGGATTTTATTTTATTTATCCTTATTGT-AATCTAAAAGGATTTTTGAGATTTTT
* *
154361 CTGTTTGTTCATATGAACAACAAACTGAAATTTGTTTC
65 ATGTTTGTTCATATGAAGAACAAACTGAAATTTGTTTC
* * * * *
154399 ATGATTTTTGAGGATTTTATTTT-TCTCT-CTTATTGT-A---AAAA-TATTTTTGTGGATTTTT
1 ATGATTTTTGGGGATTTTATTTTATTTATCCTTATTGTAATCTAAAAGGATTTTTG-AGATTTTT
* * * *
154457 TTGTTTATTCATATGAAGAACAAATTG-AATTTTTTTC
65 ATGTTTGTTCATATGAAGAACAAACTGAAATTTGTTTC
* * * *
154494 ATGATTTTTGGGGATTTTA-TTTATTTATCCTTATTTTATGTCT-AAAGGAATTTCTGGTGATTT
1 ATGATTTTTGGGGATTTTATTTTATTTATCCTTATTGTA-ATCTAAAAGG-ATTT-TTGAGATTT
*
154557 TCTATGTTTGTTCAAATGAAGAACAAACTGA
63 T-TATGTTTGTTCATATGAAGAACAAACTGA
154588 TTTCTTTTTT
Statistics
Matches: 154, Mismatches: 22, Indels: 25
0.77 0.11 0.12
Matches are distributed among these distances:
94 3 0.02
95 37 0.24
96 41 0.27
99 1 0.01
100 3 0.02
101 8 0.05
102 13 0.08
103 48 0.31
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (102 bp):
ATGATTTTTGGGGATTTTATTTTATTTATCCTTATTGTAATCTAAAAGGATTTTTGAGATTTTTA
TGTTTGTTCATATGAAGAACAAACTGAAATTTGTTTC
Found at i:165590 original size:40 final size:40
Alignment explanation
Indices: 165546--165625 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
165536 TTGGTTGTTG
* *
165546 GGGTTTGGGCTACACATTTAGTTGATGAGGGTGGTTTGGT
1 GGGTTTGGGCTACACATTTAGTTGATGAGAGTGGCTTGGT
*
165586 GGGTTTGGGCTGCACATTTAGTTGATGAGAGTGGCTTGGT
1 GGGTTTGGGCTACACATTTAGTTGATGAGAGTGGCTTGGT
165626 TGTCTGTGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.15, C:0.09, G:0.40, T:0.36
Consensus pattern (40 bp):
GGGTTTGGGCTACACATTTAGTTGATGAGAGTGGCTTGGT
Found at i:170462 original size:53 final size:53
Alignment explanation
Indices: 170399--170508 Score: 186
Period size: 53 Copynumber: 2.1 Consensus size: 53
170389 TTGAGACCTT
*
170399 ATTTATTGTTAATGATCACGATTTATGAGGAACTCTTGAAGATTTCC-GCCATG
1 ATTTATTGTTAATAATCACGATTTATGAGGAACTCTTGAAGATTTCCTG-CATG
*
170452 ATTTATTGTTAATAATTACGATTTATGAGGAACTCTTGAAGATTTCCTGCATG
1 ATTTATTGTTAATAATCACGATTTATGAGGAACTCTTGAAGATTTCCTGCATG
170505 ATTT
1 ATTT
170509 TAATAAGTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
53 53 0.98
54 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (53 bp):
ATTTATTGTTAATAATCACGATTTATGAGGAACTCTTGAAGATTTCCTGCATG
Found at i:171415 original size:2 final size:2
Alignment explanation
Indices: 171410--171447 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
171400 AAGCTTATTT
171410 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
171448 CACACGCACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:185488 original size:29 final size:29
Alignment explanation
Indices: 185451--185517 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
185441 TTCTCTGACC
* *
185451 TTAGCTATACAATGGGAAAGTAAGACCTA
1 TTAGCTATAAAATGAGAAAGTAAGACCTA
*
185480 TTAGTTATAAAATGAGAAAGTAAGACCTA
1 TTAGCTATAAAATGAGAAAGTAAGACCTA
*
185509 ATAGC-ATAA
1 TTAGCTATAA
185518 TTTGAATAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.25
Consensus pattern (29 bp):
TTAGCTATAAAATGAGAAAGTAAGACCTA
Found at i:189460 original size:17 final size:18
Alignment explanation
Indices: 189438--189471 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
189428 CATAAAATTG
*
189438 AAAATTTTA-AATACAAC
1 AAAATTATACAATACAAC
189455 AAAATTATACAATACAA
1 AAAATTATACAATACAA
189472 ACACAACTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATTATACAATACAAC
Found at i:196847 original size:1 final size:1
Alignment explanation
Indices: 196841--196865 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
196831 GGCGCGCCTC
196841 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
196866 GCACCTATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:204677 original size:2 final size:2
Alignment explanation
Indices: 204670--204706 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
204660 ATTTTAAAAC
204670 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
204707 GTGTGGTGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:205204 original size:9 final size:9
Alignment explanation
Indices: 205183--205217 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
205173 ATACCAGAAA
*
205183 TAATAATAG
1 TAATAATAT
*
205192 TAATATTAT
1 TAATAATAT
205201 TAATAATAT
1 TAATAATAT
205210 TAATAATA
1 TAATAATA
205218 ATTTTTGCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (9 bp):
TAATAATAT
Found at i:205207 original size:12 final size:12
Alignment explanation
Indices: 205181--205219 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
205171 TTATACCAGA
* *
205181 AATAATAATAGT
1 AATATTAATAAT
*
205193 AATATTATTAAT
1 AATATTAATAAT
205205 AATATTAATAAT
1 AATATTAATAAT
205217 AAT
1 AAT
205220 TTTTGCTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (12 bp):
AATATTAATAAT
Found at i:205411 original size:20 final size:20
Alignment explanation
Indices: 205386--205427 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
205376 GGTTTGTTTC
*
205386 AAATATATTTTAAATATTTT
1 AAATATAATTTAAATATTTT
*
205406 AAATATAATTTAATTATTTT
1 AAATATAATTTAAATATTTT
205426 AA
1 AA
205428 TTTATTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AAATATAATTTAAATATTTT
Found at i:205483 original size:9 final size:9
Alignment explanation
Indices: 205467--205547 Score: 78
Period size: 9 Copynumber: 8.7 Consensus size: 9
205457 AAATTAATCG
205467 AATTAATT-
1 AATTAATTA
205475 AATTAAATTA
1 AATT-AATTA
205485 ACATT--TTA
1 A-ATTAATTA
205493 AATTAATTAA
1 AATTAATT-A
205503 AATTTAAATTA
1 AA-TT-AATTA
205514 AATTAATTA
1 AATTAATTA
205523 AATTAATTA
1 AATTAATTA
*
205532 AATTAAATTT
1 AATT-AATTA
205542 AATTAA
1 AATTAA
205548 CTTTTAATTA
Statistics
Matches: 63, Mismatches: 1, Indels: 17
0.78 0.01 0.21
Matches are distributed among these distances:
7 3 0.05
8 8 0.13
9 26 0.41
10 14 0.22
11 8 0.13
12 4 0.06
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (9 bp):
AATTAATTA
Found at i:205485 original size:5 final size:5
Alignment explanation
Indices: 205467--205547 Score: 73
Period size: 5 Copynumber: 16.2 Consensus size: 5
205457 AAATTAATCG
205467 AATT- AATT- AATTA AATTA ACATTTTA AATT- AATTAA AATTTA AATTA
1 AATTA AATTA AATTA AATTA A-A--TTA AATTA AATT-A AA-TTA AATTA
*
205514 AATT- AATTA AATT- AATTA AATTA AATTT AATTA A
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA A
205548 CTTTTAATTA
Statistics
Matches: 66, Mismatches: 2, Indels: 17
0.78 0.02 0.20
Matches are distributed among these distances:
4 20 0.30
5 33 0.50
6 6 0.09
7 3 0.05
8 4 0.06
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (5 bp):
AATTA
Found at i:205516 original size:34 final size:32
Alignment explanation
Indices: 205467--205558 Score: 101
Period size: 30 Copynumber: 3.1 Consensus size: 32
205457 AAATTAATCG
205467 AATT-AATT-AATTAAATTAACATTTTAAATT
1 AATTAAATTAAATTAAATTAACATTTTAAATT
205497 AATTAAAATTTAAATTAAATT-A-A--TTAAATT
1 AATT-AAA-TTAAATTAAATTAACATTTTAAATT
*
205527 AATTAAATTAAATTTAATTAAC-TTTT-AATT
1 AATTAAATTAAATTAAATTAACATTTTAAATT
205557 AA
1 AA
205559 ATCAATTTTA
Statistics
Matches: 53, Mismatches: 1, Indels: 16
0.76 0.01 0.23
Matches are distributed among these distances:
28 11 0.21
29 4 0.08
30 21 0.40
31 2 0.04
32 3 0.06
33 3 0.06
34 9 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (32 bp):
AATTAAATTAAATTAAATTAACATTTTAAATT
Found at i:205568 original size:26 final size:26
Alignment explanation
Indices: 205525--205584 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
205515 ATTAATTAAA
*
205525 TTAATTAAATTAAATTTAA-TTAACTT
1 TTAATTAAATCAAATTTAACTT-ACTT
*
205551 TTAATTAAATCAATTTTAACTTACTT
1 TTAATTAAATCAAATTTAACTTACTT
205577 TTAATTAA
1 TTAATTAA
205585 CCCTACTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 29 0.94
27 2 0.06
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (26 bp):
TTAATTAAATCAAATTTAACTTACTT
Found at i:206397 original size:15 final size:16
Alignment explanation
Indices: 206377--206418 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
206367 ATTAGGAGGG
206377 TTTTAATTT-GAGTAT
1 TTTTAATTTAGAGTAT
*
206392 TTTTAAGTTTAGATTAT
1 TTTTAA-TTTAGAGTAT
*
206409 TTTAAATTTA
1 TTTTAATTTA
206419 ATTTATCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 7 0.30
17 10 0.43
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (16 bp):
TTTTAATTTAGAGTAT
Found at i:206441 original size:16 final size:16
Alignment explanation
Indices: 206394--206442 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
206384 TTGAGTATTT
*
206394 TTAAGTTTAGATTATT
1 TTAAGTTTAGATTATC
*
206410 TTAAATTTA-ATTTATC
1 TTAAGTTTAGA-TTATC
*
206426 TTAAGGTTAGATTATC
1 TTAAGTTTAGATTATC
206442 T
1 T
206443 CGGATTTGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 1 0.04
16 25 0.93
17 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.53
Consensus pattern (16 bp):
TTAAGTTTAGATTATC
Found at i:206918 original size:15 final size:14
Alignment explanation
Indices: 206900--206943 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
206890 TGCTAAAAAA
206900 TTAAGATTTGAATTT
1 TTAAGA-TTGAATTT
*
206915 TTAATATTGAATTT
1 TTAAGATTGAATTT
*
206929 ATAAGCATTGAATTT
1 TTAAG-ATTGAATTT
206944 GTATCATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.50
Consensus pattern (14 bp):
TTAAGATTGAATTT
Found at i:207658 original size:11 final size:11
Alignment explanation
Indices: 207638--207671 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
207628 TACATATTAA
207638 ATGA-TAATGT
1 ATGATTAATGT
207648 ATGATTAATGT
1 ATGATTAATGT
207659 ATGATTAATGT
1 ATGATTAATGT
207670 AT
1 AT
207672 ACAAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 4 0.17
11 19 0.83
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (11 bp):
ATGATTAATGT
Found at i:208701 original size:76 final size:76
Alignment explanation
Indices: 208615--208862 Score: 222
Period size: 76 Copynumber: 3.2 Consensus size: 76
208605 TATTGATACG
* * * * * *
208615 AGGTTTCCACATGACCTTAGACTTCGTTTTAAGATAGTATTACCTAAATGA-CTCTAATGGACAT
1 AGGTTTCCACATAACCCTAAACTCCGTTTTAAGATAGTATTACCTAAATAACCT-TAATAGACAT
208679 GTTTTCACGCAA
65 GTTTTCACGCAA
*
208691 AGGTTTCCACATAACCCTAAACTCCGTTTTAAGGTAGTATTACCTAAATAACCTTAATAGACATG
1 AGGTTTCCACATAACCCTAAACTCCGTTTTAAGATAGTATTACCTAAATAACCTTAATAGACATG
208756 TTTTGACACG-AA
66 TTTT--CACGCAA
* * * * ** * *
208768 A-GTTT-TAAATTACTCCAACAACTCAATTTTAAGAT-GCTTTTACCTAAATGACCTTAATAGAC
1 AGGTTTCCACATAAC-CCTA-AACTCCGTTTTAAGATAG-TATTACCTAAATAACCTTAATAGAC
*
208830 ATAGTTTGGCACG--A
63 AT-GTTT-TCACGCAA
*
208844 AGGTTTCCACATGACCCTA
1 AGGTTTCCACATAACCCTA
208863 TAGTGATGAA
Statistics
Matches: 141, Mismatches: 21, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
75 5 0.04
76 69 0.49
77 54 0.38
78 13 0.09
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (76 bp):
AGGTTTCCACATAACCCTAAACTCCGTTTTAAGATAGTATTACCTAAATAACCTTAATAGACATG
TTTTCACGCAA
Found at i:209172 original size:57 final size:58
Alignment explanation
Indices: 209079--209200 Score: 147
Period size: 57 Copynumber: 2.1 Consensus size: 58
209069 GCCAAAAAGT
* *
209079 ATGAAATTACATAACAATTCCTAAATCATGAAAAATTACTAAAATAAACTTAAAATAC
1 ATGAAATTACATAACAATTCCTAAATCAAGAAAAATTACTAAAATAAACGTAAAATAC
* ** ** * * *
209137 ATGAAATTGCATAATGATT-CTAAATCAAGGTAAATTACTAGAATAATCGTAAAATGC
1 ATGAAATTACATAACAATTCCTAAATCAAGAAAAATTACTAAAATAAACGTAAAATAC
209194 ATGAAAT
1 ATGAAAT
209201 AATGTAAGTC
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
57 38 0.70
58 16 0.30
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (58 bp):
ATGAAATTACATAACAATTCCTAAATCAAGAAAAATTACTAAAATAAACGTAAAATAC
Found at i:209307 original size:29 final size:29
Alignment explanation
Indices: 209243--209307 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
209233 AAGTAATGCT
*
209243 AGATGCATGAAATTACATAATAGTACCTA
1 AGATGCTTGAAATTACATAATAGTACCTA
209272 AGATGCTTGAAATTACATAATAGTACCTA
1 AGATGCTTGAAATTACATAATAGTACCTA
209301 AGATGCT
1 AGATGCT
209308 CTAATATAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (29 bp):
AGATGCTTGAAATTACATAATAGTACCTA
Found at i:210861 original size:20 final size:20
Alignment explanation
Indices: 210814--210866 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
210804 ACAACATTGC
** *
210814 ATCGATACAAGGGTACATTGT
1 ATCGATACAATAG-ACATTAT
210835 ATCGATACAATAGACATTAT
1 ATCGATACAATAGACATTAT
*
210855 ATTGATACAATA
1 ATCGATACAATA
210867 TGGGCCTGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (20 bp):
ATCGATACAATAGACATTAT
Found at i:212693 original size:141 final size:141
Alignment explanation
Indices: 212435--212699 Score: 363
Period size: 141 Copynumber: 1.9 Consensus size: 141
212425 TCAAATTGAG
* ** * *
212435 CTATGACTACTTTCACCCTAGTAGCAAGGTTTATATTTATAATATAACCTCAAAAAGGATATGTA
1 CTATGACCACTTTCACCCTAGTAGCAAGGTCCATATTCATAATATAACCTCAAAAAGGATACGTA
*
212500 AATGCTAGCATACAATACCATTATATTTATCCCTAATGGCAAGGTCCAAAACATAGCCAGGTCAA
66 AATGCTAGCATACAATACCATTATATTTATCCCTAATGGCAAGGTCCAAAACAAAGCCAGGTCAA
212565 ATAACACTAGA
131 ATAACACTAGA
* * * * * *
212576 CTATGACCACTTTTA-CCTCAGTGGCAAGGTCCATATTCATAATGTAACTTGAGAAAGGATACGT
1 CTATGACCACTTTCACCCT-AGTAGCAAGGTCCATATTCATAATATAACCTCAAAAAGGATACGT
* * *
212640 AAATGCTAGCATACAGTACCATTATCTTTATCCCTAATGGC-AGGATCCGAAACAAAGCCA
65 AAATGCTAGCATACAATACCATTATATTTATCCCTAATGGCAAGG-TCCAAAACAAAGCCA
212700 AATTAAAAAC
Statistics
Matches: 107, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
140 6 0.06
141 101 0.94
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.28
Consensus pattern (141 bp):
CTATGACCACTTTCACCCTAGTAGCAAGGTCCATATTCATAATATAACCTCAAAAAGGATACGTA
AATGCTAGCATACAATACCATTATATTTATCCCTAATGGCAAGGTCCAAAACAAAGCCAGGTCAA
ATAACACTAGA
Found at i:213264 original size:12 final size:12
Alignment explanation
Indices: 213247--213273 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
213237 AGAAACTAAA
213247 AAAAATAAAAAG
1 AAAAATAAAAAG
213259 AAAAATAAAAAG
1 AAAAATAAAAAG
213271 AAA
1 AAA
213274 TCATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAAATAAAAAG
Found at i:217164 original size:37 final size:36
Alignment explanation
Indices: 217095--217303 Score: 143
Period size: 37 Copynumber: 5.6 Consensus size: 36
217085 CATAGGTTAA
* * * *
217095 AACAAAAACTACAATTCTAATCCGGTGGCACGGTTCG
1 AACAAAAACCACTATTCTTA-CCAGTGGCACGGTTCG
* * *
217132 AAACAAAAATCACTATTTTTACCAGTGGCACGGGTGGGTTGG
1 -AACAAAAACCACTATTCTTACCAGTGGCAC-----GGTTCG
* * *
217174 AACAAAAACCACTATTCTTACCAATGGCACGGATCA
1 AACAAAAACCACTATTCTTACCAGTGGCACGGTTCG
* * *
217210 AGATAAAAACCA-TAAATT-TTACCGGTGGCACGGATTAG
1 A-ACAAAAACCACT--ATTCTTACCAGTGGCACGG-TTCG
* * * *
217248 GACAAAAATCACTATTCTTACCGGTGGCACGGGTCG
1 AACAAAAACCACTATTCTTACCAGTGGCACGGTTCG
*
217284 AACGAAAACCACTATTCTTA
1 AACAAAAACCACTATTCTTA
217304 ATCGGTGGCA
Statistics
Matches: 133, Mismatches: 27, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
36 27 0.20
37 54 0.41
38 20 0.15
41 27 0.20
42 5 0.04
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (36 bp):
AACAAAAACCACTATTCTTACCAGTGGCACGGTTCG
Found at i:219780 original size:21 final size:21
Alignment explanation
Indices: 219754--219797 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
219744 CATAATAGCT
*
219754 ATATAAAAAGTTAGATGAGCA
1 ATATAAAAAGTTAGATGAACA
219775 ATATAAAAAGTTAGATGAACA
1 ATATAAAAAGTTAGATGAACA
219796 AT
1 AT
219798 TCGCTTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.16, T:0.25
Consensus pattern (21 bp):
ATATAAAAAGTTAGATGAACA
Found at i:220020 original size:2 final size:2
Alignment explanation
Indices: 220013--220042 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
220003 ACTTTGTTAA
220013 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
220043 TGTTTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:224071 original size:26 final size:27
Alignment explanation
Indices: 224042--224106 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 27
224032 TTAAATATTT
224042 TATAAATAATTTTAATA-TTTAATAAA
1 TATAAATAATTTTAATACTTTAATAAA
**
224068 TAT-AA-AATTACAATACTTTAATAAA
1 TATAAATAATTTTAATACTTTAATAAA
*
224093 -ATAATTAATTTTAA
1 TATAAATAATTTTAA
224107 ATTAAATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
24 10 0.32
25 12 0.39
26 9 0.29
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (27 bp):
TATAAATAATTTTAATACTTTAATAAA
Found at i:224127 original size:15 final size:16
Alignment explanation
Indices: 224019--224119 Score: 56
Period size: 16 Copynumber: 6.6 Consensus size: 16
224009 ACATATTATT
224019 AATTAATTTTAAATTA
1 AATTAATTTTAAATTA
224035 AA-T-ATTTT--A-TA
1 AATTAATTTTAAATTA
*
224046 AA-TAATTTTAATATTT
1 AATTAATTTTAA-ATTA
* * *
224062 AATAAATATAAAATTA
1 AATTAATTTTAAATTA
* *
224078 CAA-TACTTTAATAAAAT-
1 -AATTAATTT--TAAATTA
224095 AATTAATTTTAAATTA
1 AATTAATTTTAAATTA
224111 AATTAATTT
1 AATTAATTT
224120 AATATAAAAG
Statistics
Matches: 62, Mismatches: 12, Indels: 22
0.65 0.12 0.23
Matches are distributed among these distances:
11 5 0.08
12 6 0.10
14 5 0.08
15 7 0.11
16 22 0.35
17 13 0.21
18 4 0.06
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTAATTTTAAATTA
Found at i:224217 original size:30 final size:31
Alignment explanation
Indices: 224181--224241 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
224171 CATATGTAGG
224181 CTATCATTATTTCTTCAT-AGATCCAATGGT
1 CTATCATTATTTCTTCATAAGATCCAATGGT
*
224211 CTATCATTATTTCTTCATAAGCTCCAATGGT
1 CTATCATTATTTCTTCATAAGATCCAATGGT
224242 TAATTATTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (31 bp):
CTATCATTATTTCTTCATAAGATCCAATGGT
Found at i:225668 original size:7 final size:7
Alignment explanation
Indices: 225646--225688 Score: 68
Period size: 7 Copynumber: 5.9 Consensus size: 7
225636 TCCGGATCAT
225646 TTTTTTA
1 TTTTTTA
225653 TTATTTTTA
1 -T-TTTTTA
225662 TTTTTTA
1 TTTTTTA
225669 TTTTTTA
1 TTTTTTA
225676 TTTTTTA
1 TTTTTTA
225683 TTTTTT
1 TTTTTT
225689 TTAAAAAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
7 26 0.76
8 2 0.06
9 6 0.18
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTA
Found at i:225757 original size:26 final size:24
Alignment explanation
Indices: 225708--225761 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
225698 CAAATATTCA
* *
225708 AAAAATAAAAGATAATATAGAAAT
1 AAAAATAAAAAATAATAAAGAAAT
*
225732 CAAAAATAAAAAATAAATAAATAAAT
1 -AAAAATAAAAAAT-AATAAAGAAAT
225758 AAAA
1 AAAA
225762 GTCGGGAACG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.19
Consensus pattern (24 bp):
AAAAATAAAAAATAATAAAGAAAT
Found at i:227513 original size:16 final size:15
Alignment explanation
Indices: 227482--227522 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 15
227472 AAATTAGAAT
227482 TAAAAAATAAAAAATAA
1 TAAAAAAT--AAAATAA
227499 TAACAAAATAAAATAA
1 TAA-AAAATAAAATAA
227515 TAAAAAAT
1 TAAAAAAT
227523 TCTTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
17 3 0.13
18 5 0.22
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (15 bp):
TAAAAAATAAAATAA
Found at i:231982 original size:22 final size:19
Alignment explanation
Indices: 231952--232000 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 19
231942 TTAATGGCAT
231952 TCATATTCATGACATTCATTCA
1 TCATATTCAT-A-A-TCATTCA
*
231974 TCATTTTCATAATCATTCA
1 TCATATTCATAATCATTCA
231993 TCAGTATT
1 TCA-TATT
232001 TGCTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.42
20 4 0.17
21 1 0.04
22 9 0.38
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (19 bp):
TCATATTCATAATCATTCA
Found at i:235934 original size:12 final size:12
Alignment explanation
Indices: 235919--235943 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
235909 AGGAGATACT
235919 AAGGATGATAAA
1 AAGGATGATAAA
235931 AAGGATGATAAA
1 AAGGATGATAAA
235943 A
1 A
235944 TGGGAACCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (12 bp):
AAGGATGATAAA
Found at i:240239 original size:42 final size:42
Alignment explanation
Indices: 240187--240754 Score: 674
Period size: 42 Copynumber: 13.5 Consensus size: 42
240177 TTTTTTGTTT
* * * ** *
240187 TCCCTTAGTCTGCCTGTCGGTTTTGACCTTTAAGACTTTTCT
1 TCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * * * *
240229 TCCCTTAGTCTGCCTATCAGCTTTAACCCTGGAAACTTGTCA
1 TCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
*
240271 TCCCTCAGTCTGCCTGTCGGCTTTCACCCTGGAGACTTTTCA
1 TCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * **
240313 ACCCTTAGTCTGCCTTTTAGCTTTGACCCTGGAGACTTTTCA
1 TCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
240355 TCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
1 TCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
*
240397 TCCCTCAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTTCA
1 TCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* *
240439 TCCCTCAGTCTACCTGTCGGCTTTGACCCTAGAGACTTTTCA
1 TCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* *
240481 TCCCTCAGTCTGCCTGTCAGCTTTGACCCCGGAGACTTTTCA
1 TCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * *
240523 ACCCTCAGTCTGCCTATCAGCTTTGACCTTGGAGACTTTTCA
1 TCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
**
240565 TCCCTCAGTCTGTTTGTCGGCTTTGACCCTGGAGACTTTTCA
1 TCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * * * * * *
240607 ACCCTTCAGTCTACCTGTCAGCTTCGTCCTTGGAGAC-TTTCTT
1 TCCC-TCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-A
* * *
240650 TCCCGCAGTCTGCCTGTCGGC-TTCATCCCTGGAGAC-TTTCTT
1 TCCCTCAGTCTGCCTGTCGGCTTTGA-CCCTGGAGACTTTTC-A
* * *
240692 TCCCTTAGTCTGCTTGTTGGCTTTGACCCTGGAGACTTTTCA
1 TCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* *
240734 ACCCTTCAGTCTACCTGTCGG
1 TCCC-TCAGTCTGCCTGTCGG
240755 TTTCTTCCCT
Statistics
Matches: 447, Mismatches: 73, Indels: 11
0.84 0.14 0.02
Matches are distributed among these distances:
41 1 0.00
42 399 0.89
43 47 0.11
ACGTcount: A:0.14, C:0.32, G:0.18, T:0.35
Consensus pattern (42 bp):
TCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
Found at i:240717 original size:169 final size:168
Alignment explanation
Indices: 240187--242094 Score: 2030
Period size: 169 Copynumber: 11.4 Consensus size: 168
240177 TTTTTTGTTT
* * ** * * * *
240187 TCCCTTAGTCTGCCTGTCGGTTTTGACCTTTAAGACTTTTCTTCCCTTAGTCTGCCTATCAGCTT
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGGCTT
* * * * *
240252 TAACCCTGGAAACTTGTCATCCCTCAGTCTGCCTGTCGGCTTTCACCCTGGAGACTTTTCAACCC
66 TGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCC
* **
240317 TTAGTCTGCCTTTTAGCTTTGACCCTGGAGACTTT-TCA
131 TTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCT-A
* *
240355 TCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGACTT
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGGCTT
* *
240420 TGACCCTGGAGACTTTTCATCCCTCAGTCTACCTGTCGGCTTTGACCCTAGAGACTTTTCATCCC
66 TGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCC
* * *
240485 TCAGTCTGCCTGTCAGCTTTGACCCCGGAGACTTT-TCA
131 TTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCT-A
* * * * * **
240523 ACCCTCAGTCTGCCTATCAGCTTTGACCTTGGAGACTTTTCATCCCTCAGTCTGTTTGTCGGCTT
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGGCTT
* * * * * * *
240588 TGACCCTGGAGACTTTTCAACCCTTCAGTCTACCTGTCAGCTTCGTCCTTGGAGAC-TTTCTTTC
66 TGACCCTGGAGACTTTTCATCCC-TCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-ATC
** * *
240652 CCGCAGTCTGCCTGTCGGC-TTCATCCCTGGAGACTTTCTT
129 CCTTAGTCTGCCTGTCGGCTTTGA-CCCTGGAGACTTTCTA
* * * *
240692 TCCCTTAGTCTGCTTGTTGGCTTTGACCCTGGAGACTTTTCAACCCTTCAGTCTACCTGTCGG--
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCC-TCAGTCTGCCTGTCGGCT
* * * *
240755 TT-----T-----C---T--TCCCTTAGTTTGCCTGTCGGCTTTAACCCTTGAGACTTTTCATCC
65 TTGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCC
* *
240805 CTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCT-
130 CTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCTA
* * * * * *
240844 TCCCTTAGTCTACCCGTCGGCTTTAACCCTAGAGACTTTTCTATCCCTTAGTCTGCCTGTCGGTT
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-ATCCCTCAGTCTGCCTGTCGGCT
* * * *
240909 TTGACCCTCGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCATCC
65 TTGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCC
*
240974 CTTAGTCTGCCTGTCGGTTTTGACCCTGGAGACTTTTCT-
130 CTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCTA
* * * *
241013 TTCCTTAGTCTACCTGTCGGCTTTGACCCTGGAGACTTTTCTATCCCTTAGTCTGCCTGTCGGTT
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-ATCCCTCAGTCTGCCTGTCGGCT
* * * * * *
241078 TTGACCCTAGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGTTTTGACCTTGGAGACTTTTCTTCC
65 TTGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCC
*
241143 CTTAGTTTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTA
130 CTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCTA
* * * * *
241183 TCCCTTAGTCTGCCTGTCGGTTTTGACCTTCGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTT
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGGCTT
* * * *
241248 TGACTCTAGAGACTTTTTATCCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCATCCC
66 TGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCC
* * *
241313 TCAGTCTGCCTGTCGGCTTTGACCCTAGAAACTTT-TCA
131 TTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCT-A
* * * * * *
241351 ACCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAC-TTTCTTTCCCTTAGTCTGCCTATCGGCT
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-ATCCCTCAGTCTGCCTGTCGGCT
* * ** * *
241415 TTGACCTTGGAGACTTTTCTATCCCTTAGTCTGCCTGTCGATTTTGACCTTGGAGACTTTGT-TT
65 TTGACCCTGGAGACTTTTC-ATCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT-TCAT
* *
241479 CCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTT-TCA
128 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCT-A
* * * * * * **
241520 TCCCTTAGTCTGCTTGTTGGCTTTGACCTTAGAGACTTTTCAACCCTCAGTCTGCCTATCAACTT
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGGCTT
* * * * ** *
241585 TGACCCTGGAGACTTTTCATCCCTCAGTTTACATATCAACTTTGACCCTGGAGACTTTTCAACCC
66 TGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCC
* * * *
241650 TTCAGTCTACCTGTCGGC-TTCATCCCTGGAGATTTTCTT
131 TT-AGTCTGCCTGTCGGCTTTGA-CCCTGGAGACTTTCTA
* * * * * * **
241689 TCCCGTAGTCTGCCTGTCGGCTTCGTCCCTGGAGAC-TTTCTTTCCCTTAGTCTGCCCGTCGATT
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-ATCCCTCAGTCTGCCTGTCGGCT
* ** *
241753 TTGACCCTAGAGACTTTTTTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCC
65 TTGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCC
* * *
241818 CTCAGTCTACCTGTCGGCTTTGACCTTGGAGACTTT-TCA
130 CTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCT-A
* * * *
241857 TCTCTTAGTCTGCCTGTTGGCTTTGACCCTGGAGACTTTTCATCCCTCAGTCTACCTATCGGCTT
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGGCTT
* *
241922 TGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCAACCC
66 TGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCC
* *
241987 TCAGTCTGCCTGTCGGCTTTGA-CTTGGGAGACTTTTCTTA
131 TTAGTCTGCCTGTCGGCTTTGACCCT-GGAGAC-TTTC-TA
* * * * ** *
242027 T-CCTTAGTCTGCTTGTCGGCTTTGACCATGGA-AC-TTTCTTTCCCTAAGTCTGCCCATTGGCT
1 TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-ATCCCTCAGTCTGCCTGTCGGCT
242089 TTGACC
65 TTGACC
242095 TGAGAGAATA
Statistics
Matches: 1482, Mismatches: 213, Indels: 90
0.83 0.12 0.05
Matches are distributed among these distances:
152 101 0.07
153 19 0.01
154 2 0.00
155 1 0.00
158 1 0.00
159 1 0.00
163 1 0.00
164 1 0.00
167 15 0.01
168 538 0.36
169 743 0.50
170 58 0.04
171 1 0.00
ACGTcount: A:0.14, C:0.30, G:0.19, T:0.37
Consensus pattern (168 bp):
TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGGCTT
TGACCCTGGAGACTTTTCATCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATCCC
TTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTA
Found at i:240758 original size:26 final size:26
Alignment explanation
Indices: 240729--240790 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
240719 CCTGGAGACT
240729 TTTCAACCCTTCAGTCTACCTGTCGG-
1 TTTCAACCCTT-AGTCTACCTGTCGGC
** * *
240755 TTTCTTCCCTTAGTTTGCCTGTCGGC
1 TTTCAACCCTTAGTCTACCTGTCGGC
240781 TTT-AACCCTT
1 TTTCAACCCTT
240791 GAGACTTTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 17 0.59
26 12 0.41
ACGTcount: A:0.11, C:0.32, G:0.15, T:0.42
Consensus pattern (26 bp):
TTTCAACCCTTAGTCTACCTGTCGGC
Found at i:240782 original size:68 final size:68
Alignment explanation
Indices: 240686--240821 Score: 193
Period size: 68 Copynumber: 2.0 Consensus size: 68
240676 CCCTGGAGAC
* * *
240686 TTTCTTTCCCTTAGTCTGCTTGTTGGCTTTGACCCTGGAGACTTTTCAACCCTTCAGTCTACCTG
1 TTTCTTTCCCTTAGTCTGCCTGTCGGCTTTAACCCTGGAGACTTTTCAACCC-TCAGTCTACCTG
240751 TCGG
65 TCGG
* * * *
240755 TTTC-TTCCCTTAGTTTGCCTGTCGGCTTTAACCCTTGAGACTTTTCATCCCTCAGTCTGCCTGT
1 TTTCTTTCCCTTAGTCTGCCTGTCGGCTTTAACCCTGGAGACTTTTCAACCCTCAGTCTACCTGT
240819 CGG
66 CGG
240822 CTTTGACCCT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
67 15 0.25
68 41 0.68
69 4 0.07
ACGTcount: A:0.11, C:0.30, G:0.18, T:0.40
Consensus pattern (68 bp):
TTTCTTTCCCTTAGTCTGCCTGTCGGCTTTAACCCTGGAGACTTTTCAACCCTCAGTCTACCTGT
CGG
Found at i:240812 original size:110 final size:109
Alignment explanation
Indices: 240660--240863 Score: 284
Period size: 110 Copynumber: 1.9 Consensus size: 109
240650 TCCCGCAGTC
* * * * * *
240660 TGCCTGTCGGCTTCATCCCTGGAGACTTTCTTTCCCTTAGTCTGCTTGTTGGCTTTGACCCTGGA
1 TGCCTGTCGGCTTCAACCCTGGAGACTTTCTATCCCTCAGTCTGCCTGTCGGCTTTGACCCTAGA
*
240725 GACTTTTCAACCCTTCAGTCTACCTGTCGGTTTCTTCCCTTAGTT
66 GACTTTTCAACCCTT-AGTCTACCCGTCGGTTTCTTCCCTTAGTT
* *
240770 TGCCTGTCGGCTTTAACCCTTGAGACTTT-TCATCCCTCAGTCTGCCTGTCGGCTTTGACCCTAG
1 TGCCTGTCGGCTTCAACCCTGGAGACTTTCT-ATCCCTCAGTCTGCCTGTCGGCTTTGACCCTAG
**
240834 AGACTTTTCTTCCCTTAGTCTACCCGTCGG
65 AGACTTTTCAACCCTTAGTCTACCCGTCGG
240864 CTTTAACCCT
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
109 14 0.17
110 68 0.83
ACGTcount: A:0.12, C:0.31, G:0.19, T:0.38
Consensus pattern (109 bp):
TGCCTGTCGGCTTCAACCCTGGAGACTTTCTATCCCTCAGTCTGCCTGTCGGCTTTGACCCTAGA
GACTTTTCAACCCTTAGTCTACCCGTCGGTTTCTTCCCTTAGTT
Found at i:240819 original size:42 final size:42
Alignment explanation
Indices: 240755--242094 Score: 1591
Period size: 42 Copynumber: 31.8 Consensus size: 42
240745 TACCTGTCGG
* * * *
240755 TTTCTTCCCTTAGTTTGCCTGTCGGCTTTAACCCTTGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* *
240797 TTTCATCCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * * * *
240839 TTTCTTCCCTTAGTCTACCCGTCGGCTTTAACCCTAGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* *
240881 TTTCTATCCCTTAGTCTGCCTGTCGGTTTTGACCCTCGAGACT
1 TTTC-ATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* *
240924 TTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
*
240966 TTTCATCCCTTAGTCTGCCTGTCGGTTTTGACCCTGGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * *
241008 TTTCTTTCCTTAGTCTACCTGTCGGCTTTGACCCTGGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* *
241050 TTTCTATCCCTTAGTCTGCCTGTCGGTTTTGACCCTAGAGACT
1 TTTC-ATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * *
241093 TTTCTTCCCTTAGTCTGCCTGTCGGTTTTGACCTTGGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* *
241135 TTTCTTCCCTTAGTTTGCCTGTCGGCTTTGACCCTGGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * *
241177 TTTCTATCCCTTAGTCTGCCTGTCGGTTTTGACCTTCGAGACT
1 TTTC-ATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * *
241220 TTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACTCTAGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * *
241262 TTTTATCCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * *
241304 TTTCATCCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAAACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * *
241346 TTTCAACCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAC-
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * *
241387 TTTCTTTCCCTTAGTCTGCCTATCGGCTTTGACCTTGGAGACT
1 TTTC-ATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
** *
241430 TTTCTATCCCTTAGTCTGCCTGTCGATTTTGACCTTGGAGACT
1 TTTC-ATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * *
241473 TTGT-TTCCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACT
1 TT-TCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * * *
241515 TTTCATCCCTTAGTCTGCTTGTTGGCTTTGACCTTAGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * * **
241557 TTTCAACCCTCAGTCTGCCTATCAACTTTGACCCTGGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * * * * **
241599 TTTCATCCCTCAGTTTACATATCAACTTTGACCCTGGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * *
241641 TTTCAACCCTTCAGTCTACCTGTCGGC-TTCATCCCTGGAGA-T
1 TTTCATCCCTT-AGTCTGCCTGTCGGCTTTGA-CCCTGGAGACT
* * * *
241683 TTTCTTTCCCGTAGTCTGCCTGTCGGCTTCGTCCCTGGAGAC-
1 TTTC-ATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * ** *
241725 TTTCTTTCCCTTAGTCTGCCCGTCGATTTTGACCCTAGAGACT
1 TTTC-ATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
**
241768 TTTTTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * *
241810 TTTCATCCCTCAGTCTACCTGTCGGCTTTGACCTTGGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* *
241852 TTTCATCTCTTAGTCTGCCTGTTGGCTTTGACCCTGGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * *
241894 TTTCATCCCTCAGTCTACCTATCGGCTTTGACCCTGGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* *
241936 TTTCATCCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * *
241978 TTTCAACCCTCAGTCTGCCTGTCGGCTTTGA-CTTGGGAGACT
1 TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCT-GGAGACT
* *
242020 TTTCTTAT-CCTTAGTCTGCTTGTCGGCTTTGACCATGGA-AC-
1 TTTC--ATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * ** *
242061 TTTCTTTCCCTAAGTCTGCCCATTGGCTTTGACC
1 TTTC-ATCCCTTAGTCTGCCTGTCGGCTTTGACC
242095 TGAGAGAATA
Statistics
Matches: 1135, Mismatches: 145, Indels: 37
0.86 0.11 0.03
Matches are distributed among these distances:
40 2 0.00
41 32 0.03
42 894 0.79
43 203 0.18
44 4 0.00
ACGTcount: A:0.14, C:0.30, G:0.19, T:0.38
Consensus pattern (42 bp):
TTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
Found at i:242197 original size:15 final size:17
Alignment explanation
Indices: 242177--242208 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
242167 AACTGTGTGG
242177 TCCTGC-TT-TTGTTTT
1 TCCTGCATTCTTGTTTT
242192 TCCTGCATTCTTGTTTT
1 TCCTGCATTCTTGTTTT
242209 ATTCTTCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.03, C:0.22, G:0.12, T:0.62
Consensus pattern (17 bp):
TCCTGCATTCTTGTTTT
Found at i:243300 original size:16 final size:17
Alignment explanation
Indices: 243280--243333 Score: 56
Period size: 19 Copynumber: 3.1 Consensus size: 17
243270 TTTCCTTCCG
243280 ACTTCCATTCCAACAGC
1 ACTTCCATTCCAACAGC
*
243297 -CTTCCATCCACAACAGC
1 ACTTCCATTC-CAACAGC
*
243314 AGCTTCCAACTCCAACAGC
1 A-CTTCC-ATTCCAACAGC
243333 A
1 A
243334 TTAAACAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 8 0.27
17 7 0.23
19 13 0.43
20 2 0.07
ACGTcount: A:0.31, C:0.43, G:0.07, T:0.19
Consensus pattern (17 bp):
ACTTCCATTCCAACAGC
Found at i:244167 original size:16 final size:15
Alignment explanation
Indices: 244146--244176 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
244136 TACAAAATAA
244146 AAAATAATAACAAAAT
1 AAAATAATAA-AAAAT
244162 AAAATAATAAAAAAT
1 AAAATAATAAAAAAT
244177 TCTTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATAATAAAAAAT
Found at i:246646 original size:2 final size:2
Alignment explanation
Indices: 246639--246685 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
246629 TTCCTATAAG
* *
246639 AT AT AT AT AT AT AT AT AT AC AT AT AT AC 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 AT AT AT
246681 AT AT A
1 AT AT A
246686 AACACACTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:246939 original size:4 final size:4
Alignment explanation
Indices: 246930--246956 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
246920 AATTCATTGT
246930 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
246957 TTTGCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:248719 original size:3 final size:3
Alignment explanation
Indices: 248713--248746 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
248703 ATAATAATAT
*
248713 TTA TTA TTC TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
248747 CAAATTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:252417 original size:21 final size:21
Alignment explanation
Indices: 252380--252419 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
252370 ATTTTTTATT
*
252380 TAAATTTAATTATAAAATATA
1 TAAATTTAATTAAAAAATATA
252401 TAAATATTAA-TAAAAAATA
1 TAAAT-TTAATTAAAAAATA
252420 AATTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTTAATTAAAAAATATA
Found at i:256036 original size:2 final size:2
Alignment explanation
Indices: 256029--256055 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
256019 CATTAAATTA
256029 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
256056 AATCTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:258841 original size:19 final size:18
Alignment explanation
Indices: 258791--258841 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 18
258781 AATATTTCAT
*
258791 ATAAAAT-TA-CAATATA
1 ATAAAATATATCAATTTA
*
258807 ATAAAATATATAAATTTA
1 ATAAAATATATCAATTTA
*
258825 ATATAAATCTATCAATT
1 ATA-AAATATATCAATT
258842 AGCAAAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 7 0.25
17 2 0.07
18 8 0.29
19 11 0.39
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAAAATATATCAATTTA
Found at i:259212 original size:18 final size:18
Alignment explanation
Indices: 259189--259224 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
259179 CGGTCTGTTT
259189 ACGAATAAATAGCTACTG
1 ACGAATAAATAGCTACTG
259207 ACGAATAAATAGCTACTG
1 ACGAATAAATAGCTACTG
259225 CAACTGCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (18 bp):
ACGAATAAATAGCTACTG
Found at i:267208 original size:14 final size:16
Alignment explanation
Indices: 267174--267211 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
267164 AAAAAGTGAT
*
267174 AAGTCAATTATAGATA
1 AAGTCAACTATAGATA
267190 AAGTCAACTATA-A-A
1 AAGTCAACTATAGATA
267204 AAGTCAAC
1 AAGTCAAC
267212 CTTTTGGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 11 0.52
ACGTcount: A:0.53, C:0.13, G:0.11, T:0.24
Consensus pattern (16 bp):
AAGTCAACTATAGATA
Found at i:277622 original size:23 final size:22
Alignment explanation
Indices: 277586--277629 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
277576 GATATTTTCC
277586 ATATTAAGATTTATATTTTAAAT
1 ATATTAAGATTTAT-TTTTAAAT
277609 ATATTAA-ATATTATTTTTAAA
1 ATATTAAGAT-TTATTTTTAAA
277630 AAATGATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATTAAGATTTATTTTTAAAT
Found at i:281181 original size:2 final size:2
Alignment explanation
Indices: 281168--281203 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
281158 GTTGTGCCAG
* *
281168 AT AT AT AC AT AT AT TT 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
281204 TACTATTATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:282294 original size:23 final size:23
Alignment explanation
Indices: 282268--282312 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
282258 ATCAAAGTAA
282268 GCGAGAATTAGTGCATATTCATT
1 GCGAGAATTAGTGCATATTCATT
282291 GCGAGAATTAGTGCATATTCAT
1 GCGAGAATTAGTGCATATTCAT
282313 AATTATTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.33
Consensus pattern (23 bp):
GCGAGAATTAGTGCATATTCATT
Done.