Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008235.1 Hibiscus syriacus cultivar Beakdansim tig00110879_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 820011
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:236905 original size:54 final size:54
Alignment explanation
Indices: 236823--236978 Score: 258
Period size: 54 Copynumber: 2.9 Consensus size: 54
236813 AGAATAGCAG
***
236823 GTTCGTAAAACATTTGACAGTGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* *
236877 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
*
236931 GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
236979 CAAGATTTCT
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 94 1.00
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:239097 original size:114 final size:114
Alignment explanation
Indices: 238897--239119 Score: 392
Period size: 114 Copynumber: 2.0 Consensus size: 114
238887 GATCATGCAG
* * *
238897 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAGTCCAATGATTGGTTCTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
*
238962 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
*
239011 TTCATCTTTCAAGTCCAATGATTGGTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAGTCCAATGATTGGTTCTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
*
239076 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGA
239120 TCACATGGCA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAGTCCAATGATTGGTTCTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:243555 original size:17 final size:17
Alignment explanation
Indices: 243533--243567 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
243523 AAGGCTATTC
243533 TTTGGGTTCAATTGGGA
1 TTTGGGTTCAATTGGGA
243550 TTTGGGTTCAATTGGGA
1 TTTGGGTTCAATTGGGA
243567 T
1 T
243568 GCCCCAGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.06, G:0.34, T:0.43
Consensus pattern (17 bp):
TTTGGGTTCAATTGGGA
Found at i:247154 original size:22 final size:22
Alignment explanation
Indices: 247136--247178 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
247126 AAAATTAATC
*
247136 AAATAATATATTAATATTATTAA
1 AAATAATA-ATTAATATTAATAA
*
247159 AAATAATAATTATTATTAAT
1 AAATAATAATTAATATTAAT
247179 TTAAATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAATAATAATTAATATTAATAA
Found at i:248317 original size:3 final size:3
Alignment explanation
Indices: 248295--248345 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
248285 TGGACCGTTG
* *
248295 TAA TAA T-A TATA TAA T-A TAA TAA TAA TAT TTA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
248339 TAA TAA T
1 TAA TAA T
248346 TTTAGTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:248332 original size:18 final size:20
Alignment explanation
Indices: 248295--248343 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
248285 TGGACCGTTG
248295 TAATAATATATATAATATAA
1 TAATAATATATATAATATAA
*
248315 TAATAATATTTATAATAATAA
1 TAATAATATATATAAT-ATAA
248336 TAATAATA
1 TAATAATA
248344 ATTTTAGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAATAATATATATAATATAA
Found at i:249007 original size:32 final size:32
Alignment explanation
Indices: 248966--249030 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
248956 TTGCATGGAC
*
248966 TACATAATCCACAGTAAAATATCCTAGAAGTG
1 TACAGAATCCACAGTAAAATATCCTAGAAGTG
* *
248998 TACAGAATCCACTGTTAAATATCCTAGAAGTG
1 TACAGAATCCACAGTAAAATATCCTAGAAGTG
249030 T
1 T
249031 TGGGGAGCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TACAGAATCCACAGTAAAATATCCTAGAAGTG
Found at i:257933 original size:42 final size:42
Alignment explanation
Indices: 257897--258169 Score: 287
Period size: 42 Copynumber: 6.5 Consensus size: 42
257887 AAGACGTGAC
* * * * *
257897 CGTTCCTACTCTCCTGATGATAGATGCTACAGAAGACGGGAT
1 CGTTCCTACTCACCAGATGATCGATACTACAGAAGGCGGGAT
* * * * * * * * *
257939 AGGTCTTACACTCCAGATGAAC-ATTACTACCGTAGGCGAGAT
1 CGTTCCTACTCACCAGATGATCGA-TACTACAGAAGGCGGGAT
* * *
257981 CGTTCCTACTCACCTGATGATCGATGCTATAGAAGGCGGGAT
1 CGTTCCTACTCACCAGATGATCGATACTACAGAAGGCGGGAT
* * **
258023 CGTTCCTATTCACGAGATGATCGATACTGTAGAAGGCGGGAT
1 CGTTCCTACTCACCAGATGATCGATACTACAGAAGGCGGGAT
* *
258065 CGTTCCTACTCACCAGAAGATCGGTACTACAGAAGGCGGGAT
1 CGTTCCTACTCACCAGATGATCGATACTACAGAAGGCGGGAT
* * *
258107 CGTTCCTACTCACCAGAAGATCGGTACTACAGAAGGCGAGAT
1 CGTTCCTACTCACCAGATGATCGATACTACAGAAGGCGGGAT
*
258149 CGTTCCTACTCTCCAGATGAT
1 CGTTCCTACTCACCAGATGAT
258170 AGTCACAGTA
Statistics
Matches: 191, Mismatches: 38, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
41 1 0.01
42 189 0.99
43 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (42 bp):
CGTTCCTACTCACCAGATGATCGATACTACAGAAGGCGGGAT
Found at i:262830 original size:20 final size:20
Alignment explanation
Indices: 262801--262846 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
262791 TCGTTGGATT
*
262801 ATTTTGATGTTTAAAAATCG
1 ATTTTAATGTTTAAAAATCG
*
262821 ATTTTAATGTTTAAAAATTG
1 ATTTTAATGTTTAAAAATCG
262841 ATTTTA
1 ATTTTA
262847 GATTATAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (20 bp):
ATTTTAATGTTTAAAAATCG
Found at i:264091 original size:35 final size:33
Alignment explanation
Indices: 264051--264135 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
264041 GTATTTCAGT
*
264051 TAATTTTGTT-TATTATCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
264086 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
264121 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
264136 TAAAATTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 2 0.05
38 12 0.29
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Found at i:266040 original size:14 final size:14
Alignment explanation
Indices: 265993--266040 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
265983 ATATTTAAAA
*
265993 AAAAAAATCATAAT
1 AAAAAAATTATAAT
*
266007 AAACAATAAGTATAAT
1 AAA-AA-AATTATAAT
*
266023 AAAAAAATTATAAC
1 AAAAAAATTATAAT
266037 AAAA
1 AAAA
266041 TTACCTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 14 0.50
15 4 0.14
16 10 0.36
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.21
Consensus pattern (14 bp):
AAAAAAATTATAAT
Found at i:268490 original size:29 final size:29
Alignment explanation
Indices: 268446--268504 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
268436 ATTTTCACCT
*
268446 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGACGTAAGCAATGACATCAA
268475 AACTAAATTGACGTAAGCAATGACATCAA
1 AACTAAATTGACGTAAGCAATGACATCAA
268504 A
1 A
268505 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.22
Consensus pattern (29 bp):
AACTAAATTGACGTAAGCAATGACATCAA
Found at i:273163 original size:27 final size:28
Alignment explanation
Indices: 273121--273177 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 28
273111 ATTTTCACCT
273121 AACTAAATTGATGTAAGCAATGACATCA
1 AACTAAATTGATGTAAGCAATGACATCA
273149 AACTAAA-TGATGTAAGCAATGACATCA
1 AACTAAATTGATGTAAGCAATGACATCA
273176 AA
1 AA
273178 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (28 bp):
AACTAAATTGATGTAAGCAATGACATCA
Found at i:275793 original size:31 final size:31
Alignment explanation
Indices: 275755--275877 Score: 219
Period size: 31 Copynumber: 4.0 Consensus size: 31
275745 GGGTCGAGGG
275755 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
275786 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
275817 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* * *
275848 TTACCTAGGTTCTTCGGAATATATGGACTG
1 TTACCTATGTTCTTCGGGACATATGGACTG
275878 GTCCTTCGGG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 89 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:279570 original size:31 final size:31
Alignment explanation
Indices: 279532--279637 Score: 180
Period size: 31 Copynumber: 3.5 Consensus size: 31
279522 GGGTCGAGGG
279532 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
279563 TTACCTATGTTC-TC-GGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
279592 TTACCTATGTTCTTTGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
279623 TTACCTAGGTTCTTC
1 TTACCTATGTTCTTC
279638 AGAATCTATG
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
29 27 0.39
30 3 0.04
31 40 0.57
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.41
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:279967 original size:184 final size:184
Alignment explanation
Indices: 279597--279969 Score: 730
Period size: 185 Copynumber: 2.0 Consensus size: 184
279587 ACTGTTTACC
279597 TATGTTCTTTGGGACATATGGACTGTTTACCTAGGTTCTTCAGAATCTATGGACTGGTCCTTCGG
1 TATGTTCTTTGGGACATATGGACTGTTTACCTAGGTTCTTCAGAATCTATGGACTGGTCCTTCGG
279662 ACATTGATCGAGCTGTGGTGACAGCATATGTGTGCACAACCTCAATGTACTCACATACCTTAAGT
66 ACATTGATCGAGCTGTGGTGACAGCATATGTGTGCACAACCTCAATGTACTCACATACCTTAAGT
279727 TCTCACTAGTGTACATGGGCTAATAAAGTGATTAAACAAGCATACTGAATGTGA
131 TCTCACTAGTGTACATGGGCTAATAAAGTGATTAAACAAGCATACTGAATGTGA
279781 TATGTTCTTTGGGACATATGGACTGTTTACCTAGGTTCTTCAGAATCTATGGACTGGTCCTTCGG
1 TATGTTCTTTGGGACATATGGACTGTTTACCTAGGTTCTTCAGAATCTATGGACTGGTCCTTC-G
279846 GACATTGATCGAGCTGTGGTGACAGCATATGTGTGCACAACCTCAATGTACTCACATACCTTAAG
65 GACATTGATCGAGCTGTGGTGACAGCATATGTGTGCACAACCTCAATGTACTCACATACCTTAAG
279911 TTCTCACTAGTGTACATGGGCTAATAAAGTGATTAAACAAGCATACTGAA-GTGA
130 TTCTCACTAGTGTACATGGGCTAATAAAGTGATTAAACAAGCATACTGAATGTGA
279965 TATGT
1 TATGT
279970 ATACGATGGG
Statistics
Matches: 188, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
184 72 0.38
185 116 0.62
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.32
Consensus pattern (184 bp):
TATGTTCTTTGGGACATATGGACTGTTTACCTAGGTTCTTCAGAATCTATGGACTGGTCCTTCGG
ACATTGATCGAGCTGTGGTGACAGCATATGTGTGCACAACCTCAATGTACTCACATACCTTAAGT
TCTCACTAGTGTACATGGGCTAATAAAGTGATTAAACAAGCATACTGAATGTGA
Found at i:283645 original size:14 final size:15
Alignment explanation
Indices: 283630--283679 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
283620 TATTATCAAA
283630 TATTTAAACACTAA-
1 TATTTAAACACTAAT
*
283644 TATTTAAATA-TAAAT
1 TATTTAAACACT-AAT
*
283659 TATGTAAACACTAAT
1 TATTTAAACACTAAT
283674 TATTTA
1 TATTTA
283680 GATGAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 1 0.03
14 11 0.38
15 16 0.55
16 1 0.03
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (15 bp):
TATTTAAACACTAAT
Found at i:284912 original size:2 final size:2
Alignment explanation
Indices: 284907--284941 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
284897 ATGTATTGAG
284907 AT AT AT AT 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 AT AT AT AT A
284942 AATAGTTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:290866 original size:3 final size:3
Alignment explanation
Indices: 290858--290905 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
290848 GTCGTTGCAG
290858 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
290906 GGGCCGTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:294908 original size:150 final size:144
Alignment explanation
Indices: 294640--294925 Score: 385
Period size: 150 Copynumber: 1.9 Consensus size: 144
294630 GTACCTCTCG
* *
294640 TTCTTTTGCACTTTCAACAATGCTTGTATATTCAATTGTTTCTGTTTCGTTCATACCAGCTTCTT
1 TTCTTTTGCACTTCCAACAATGCTTGTATATTCAATTGTTTCTGTTTCGTTAATACCAGCTTCTT
** * *
294705 GTTCATTTGATTTTTCAGGTTCACTGATGTCTTCCGGTCTGACTAAGAGTAGGGATTCACCTTCA
66 GTTCATTTGATTTTTCAGGGCCACTGACGTCTTCCGGTCTGACTAAGAATAGGGATTCACCTTCA
*
294770 TTAGCTTTCTCCTT
131 CTAGCTTTCTCCTT
* **
294784 TTCTTTTGCACTTCCAACAATTCTTGTATAATCACTTTCAATTGTTTCTGTTTCGTTAATGTCAG
1 TTCTTTTGCACTTCCAACAATGCTTG--T-AT-A--TTCAATTGTTTCTGTTTCGTTAATACCAG
* * *
294849 CTTCTTGTTCATTTGATTTTTC-GGAGCCGCTGGCGTCTTCCGGTCTGATTAAGAATAGGGATTC
60 CTTCTTGTTCATTTGATTTTTCAGG-GCCACTGACGTCTTCCGGTCTGACTAAGAATAGGGATTC
294913 ACCTTCACTAGCT
124 ACCTTCACTAGCT
294926 GACAACTCCT
Statistics
Matches: 122, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
144 24 0.20
146 1 0.01
147 2 0.02
148 1 0.01
149 2 0.02
150 92 0.75
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.44
Consensus pattern (144 bp):
TTCTTTTGCACTTCCAACAATGCTTGTATATTCAATTGTTTCTGTTTCGTTAATACCAGCTTCTT
GTTCATTTGATTTTTCAGGGCCACTGACGTCTTCCGGTCTGACTAAGAATAGGGATTCACCTTCA
CTAGCTTTCTCCTT
Found at i:308604 original size:14 final size:14
Alignment explanation
Indices: 308582--308615 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
308572 TTCACTCAAT
*
308582 AAATATATATTTAA
1 AAATTTATATTTAA
308596 AAATTTATATTTAA
1 AAATTTATATTTAA
308610 ACAATT
1 A-AATT
308616 GAAAACATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTTATATTTAA
Found at i:310050 original size:28 final size:28
Alignment explanation
Indices: 310010--310073 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
310000 ACAAAGCACA
310010 GAACACAATCAATGGTTCTATTCGACCT
1 GAACACAATCAATGGTTCTATTCGACCT
310038 GAACACAATCAATGGTTCTATTCGACCT
1 GAACACAATCAATGGTTCTATTCGACCT
*
310066 GCACACAA
1 GAACACAA
310074 AGAATACATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (28 bp):
GAACACAATCAATGGTTCTATTCGACCT
Found at i:310225 original size:17 final size:17
Alignment explanation
Indices: 310203--310239 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
310193 ATCTGCCCTC
310203 CCATTTTGATTTTTGTT
1 CCATTTTGATTTTTGTT
310220 CCATTTTGATTTTTGTT
1 CCATTTTGATTTTTGTT
310237 CCA
1 CCA
310240 CTTCCCTCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.14, C:0.16, G:0.11, T:0.59
Consensus pattern (17 bp):
CCATTTTGATTTTTGTT
Found at i:312556 original size:22 final size:22
Alignment explanation
Indices: 312530--312582 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
312520 TTTTCACGTT
*
312530 TTCAAAAGCTAATATTTTCCTA
1 TTCAAAACCTAATATTTTCCTA
* *
312552 TTCAAAACCTATTATTTTTCTA
1 TTCAAAACCTAATATTTTCCTA
*
312574 TTCGAAACC
1 TTCAAAACC
312583 GGAAAACAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.42
Consensus pattern (22 bp):
TTCAAAACCTAATATTTTCCTA
Found at i:316737 original size:28 final size:29
Alignment explanation
Indices: 316706--316768 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
316696 ATGGTCCCTC
*
316706 GACTGA-GAAAGTTACAAAATAGTCTTTT
1 GACTGATGAAAGTTACAAAATAATCTTTT
*
316734 GACT-ATTGAAAGTTACAAAATAATTTTTT
1 GACTGA-TGAAAGTTACAAAATAATCTTTT
316763 GACTGA
1 GACTGA
316769 AAGGTGTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 1 0.03
28 4 0.13
29 24 0.80
30 1 0.03
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.35
Consensus pattern (29 bp):
GACTGATGAAAGTTACAAAATAATCTTTT
Found at i:317619 original size:112 final size:109
Alignment explanation
Indices: 317414--317634 Score: 370
Period size: 112 Copynumber: 2.0 Consensus size: 109
317404 AGGGTAAACA
* *
317414 AATAGTGATCCGATTCATGATATTCCATCACCAGCAGAAAATATACAAGCACAGTACGTAGTTTC
1 AATAGTGATCCGATTCATGATATTCAATCACCAGCAAAAAATATACAAGCACAGTACGTAGTTTC
317479 TGTATAATCACTGTTGCATGGAATGTTGCAATATGTATACACAG
66 TGTATAATCACTGTTGCATGGAATGTTGCAATATGTATACACAG
*
317523 AATAGTGATCCGATTCATGATATTCAATCACTAGCAAAAAATATACAAGAAGCACAGTACGTAGT
1 AATAGTGATCCGATTCATGATATTCAATCACCAGCAAAAAATATAC---AAGCACAGTACGTAGT
* *
317588 TTCTGTCTAATTACTGTTGCATGGAATGTTGCAATATGTATACACAG
63 TTCTGTATAATCACTGTTGCATGGAATGTTGCAATATGTATACACAG
317635 TAACTTTCTT
Statistics
Matches: 104, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
109 43 0.41
112 61 0.59
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (109 bp):
AATAGTGATCCGATTCATGATATTCAATCACCAGCAAAAAATATACAAGCACAGTACGTAGTTTC
TGTATAATCACTGTTGCATGGAATGTTGCAATATGTATACACAG
Found at i:328729 original size:60 final size:61
Alignment explanation
Indices: 328642--328820 Score: 170
Period size: 61 Copynumber: 3.0 Consensus size: 61
328632 GCATCATATG
* * * * *
328642 TCCC-CAAATTATGATTATTATTTTAAATT-GGTCTTGAAA-TGTTTGAATATTTTAATTTCA
1 TCCCTCAAATTATGACTCTCATTCTAAATTAGGTCTT-AAACT-TTTGAATATTCTAATTTCA
*
328702 T-CCTCAAATTATGACTCTCATTCTAAATTAGTTCTTAAACTTTTGAATATTCTAATTTCA
1 TCCCTCAAATTATGACTCTCATTCTAAATTAGGTCTTAAACTTTTGAATATTCTAATTTCA
* * * * ** * *
328762 TCCCTAAAATTATGACCCTCTTTCAAAATTA-GTCCCCAAAATTTTGAATATTCCAATTT
1 TCCCTCAAATTATGACTCTCATTCTAAATTAGGT-CTTAAACTTTTGAATATTCTAATTT
328821 TATACCCAAA
Statistics
Matches: 99, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
59 2 0.02
60 45 0.45
61 52 0.53
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (61 bp):
TCCCTCAAATTATGACTCTCATTCTAAATTAGGTCTTAAACTTTTGAATATTCTAATTTCA
Found at i:328807 original size:61 final size:60
Alignment explanation
Indices: 328678--328820 Score: 178
Period size: 61 Copynumber: 2.4 Consensus size: 60
328668 ATTGGTCTTG
* * * * * **
328678 AAATGTTTGAATATTTTAATTTCATCCTCAAATTATGACTCTCATTCTAAATTAGTTCTTA
1 AAAT-TTTGAATATTCTAATTTCATCCTAAAATTATGACCCTCATTCAAAATTAGTCCCCA
* *
328739 AACTTTTGAATATTCTAATTTCATCCCTAAAATTATGACCCTCTTTCAAAATTAGTCCCCA
1 AAATTTTGAATATTCTAATTTCAT-CCTAAAATTATGACCCTCATTCAAAATTAGTCCCCA
*
328800 AAATTTTGAATATTCCAATTT
1 AAATTTTGAATATTCTAATTT
328821 TATACCCAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
60 19 0.27
61 51 0.73
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.43
Consensus pattern (60 bp):
AAATTTTGAATATTCTAATTTCATCCTAAAATTATGACCCTCATTCAAAATTAGTCCCCA
Found at i:329057 original size:60 final size:60
Alignment explanation
Indices: 328949--329104 Score: 176
Period size: 60 Copynumber: 2.6 Consensus size: 60
328939 GTATATGCGT
* * * *
328949 ATAGTTTG-GGATGAAATTAGAATGTTCAAAAAGTTCGGAGATTGATTTAGAATGA-AGGTC
1 ATAGTTTGAGGATGAAATTAAAATGTTC-AAAAGTTTGGAGACTAATTTAGAATGATA-GTC
*
329009 ATAGTTTGAGGATGAAACTAAAATGTTCAAAAGTTT-GAGGACTAATTTAGAATGATAGTC
1 ATAGTTTGAGGATGAAATTAAAATGTTCAAAAGTTTGGA-GACTAATTTAGAATGATAGTC
* * *
329069 ATAATTT-ATGGATGAAATTAAAATATTTAAAAGTTT
1 ATAGTTTGA-GGATGAAATTAAAATGTTCAAAAGTTT
329105 AAGAATCAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
59 3 0.04
60 62 0.75
61 18 0.22
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.34
Consensus pattern (60 bp):
ATAGTTTGAGGATGAAATTAAAATGTTCAAAAGTTTGGAGACTAATTTAGAATGATAGTC
Found at i:329116 original size:60 final size:60
Alignment explanation
Indices: 328993--329140 Score: 151
Period size: 60 Copynumber: 2.5 Consensus size: 60
328983 TCGGAGATTG
* * * *
328993 ATTTAGAATGAAGGTCATAGTTTGAGGATGAAACTAAAATGTTCAAAAGTTTGAGGACTA
1 ATTTAGAATGAAGGTCATAATTTGAGGATGAAACTAAAATATTCAAAAGTTTAAGAACTA
* *
329053 ATTTAGAATGATA-GTCATAATTT-ATGGATGAAATTAAAATATTTAAAAGTTTAAGAA-TCA
1 ATTTAGAATGA-AGGTCATAATTTGA-GGATGAAACTAAAATATTCAAAAGTTTAAGAACT-A
* * *
329113 ATTTAAAACT-AAGATCATACTTTGAGGA
1 ATTTAGAA-TGAAGGTCATAATTTGAGGA
329141 CATGTTATGC
Statistics
Matches: 73, Mismatches: 9, Indels: 12
0.78 0.10 0.13
Matches are distributed among these distances:
59 3 0.04
60 67 0.92
61 3 0.04
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (60 bp):
ATTTAGAATGAAGGTCATAATTTGAGGATGAAACTAAAATATTCAAAAGTTTAAGAACTA
Found at i:336039 original size:11 final size:11
Alignment explanation
Indices: 336009--336060 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
335999 AAAATTCAGG
*
336009 AGCTCGATCGA
1 AGCTCGATTGA
336020 AGCTCGATTGA
1 AGCTCGATTGA
336031 AGCTCGATTTTG-
1 AGCTCGA--TTGA
*
336043 AGCTCGATTCA
1 AGCTCGATTGA
336054 AGCTCGA
1 AGCTCGA
336061 ACTCAAACTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 2 0.06
11 24 0.67
12 7 0.19
13 3 0.08
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:338579 original size:22 final size:22
Alignment explanation
Indices: 338553--338594 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
338543 AGTATGTGCA
338553 GGGGGAATAGATTCCCCCCTGG
1 GGGGGAATAGATTCCCCCCTGG
* **
338575 GGGGGTATCTATTCCCCCCT
1 GGGGGAATAGATTCCCCCCT
338595 AAATGAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.31, G:0.31, T:0.24
Consensus pattern (22 bp):
GGGGGAATAGATTCCCCCCTGG
Found at i:339256 original size:44 final size:43
Alignment explanation
Indices: 339153--339265 Score: 111
Period size: 44 Copynumber: 2.6 Consensus size: 43
339143 TTACATGAAC
* * * *
339153 ACATGAGAAATAATATAAGTTATATGATACGATTTATATGATT
1 ACATGAGAAAGAATATATGTTATATGATACGATCTATATGACT
* * *
339196 ACATGCA-CATGTAATATATGTTATATGATATGGATCTATATGACT
1 ACATG-AGAAAG-AATATATGTTATATGATA-CGATCTATATGACT
*
339241 ACGTGAGAAAGAATATATGTCTATA
1 ACATGAGAAAGAATATATGT-TATA
339266 AGAAGACATA
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
43 6 0.11
44 28 0.51
45 21 0.38
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (43 bp):
ACATGAGAAAGAATATATGTTATATGATACGATCTATATGACT
Found at i:339632 original size:23 final size:24
Alignment explanation
Indices: 339598--339691 Score: 88
Period size: 23 Copynumber: 4.0 Consensus size: 24
339588 AAATCTTATA
*
339598 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
339621 TGGCACTTCGGTGCAATTT-TACG
1 TGGCACTTCGGTGCAATTTCTACG
* * *
339644 CGGTC-CTTCGG-GATAAATTCTACG
1 TGG-CACTTCGGTG-CAATTTCTACG
* *
339668 TGACACTTCGGTGCAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
339692 AGCTGTGGTG
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
22 1 0.02
23 30 0.54
24 24 0.43
25 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.32
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:345289 original size:16 final size:17
Alignment explanation
Indices: 345255--345294 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
345245 TTATATGAAC
*
345255 TGATATGTGTTTATATG
1 TGATATGTGATTATATG
*
345272 TGCTATGTGATT-TATG
1 TGATATGTGATTATATG
345288 TGATATG
1 TGATATG
345295 CCATATGTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.03, G:0.25, T:0.50
Consensus pattern (17 bp):
TGATATGTGATTATATG
Found at i:346548 original size:2 final size:2
Alignment explanation
Indices: 346541--346595 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
346531 GTTTTAAATG
346541 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
346583 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
346596 GTAAATGGTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:346703 original size:21 final size:22
Alignment explanation
Indices: 346677--346718 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
346667 TAGCAATACC
*
346677 GTAGCA-GGGTATCGGTTCCCT
1 GTAGCAGGGGAATCGGTTCCCT
346698 GTAGCAGGGGAATCGGTTCCC
1 GTAGCAGGGGAATCGGTTCCC
346719 CTCTTTGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.17, C:0.24, G:0.36, T:0.24
Consensus pattern (22 bp):
GTAGCAGGGGAATCGGTTCCCT
Found at i:347964 original size:7 final size:7
Alignment explanation
Indices: 347952--348107 Score: 69
Period size: 7 Copynumber: 22.3 Consensus size: 7
347942 CATAATCAAC
347952 TTTAGGG
1 TTTAGGG
347959 TTTAGGG
1 TTTAGGG
***
347966 AGGAGGG
1 TTTAGGG
347973 TTTAGGG
1 TTTAGGG
***
347980 TTTTTAG
1 TTTAGGG
*
347987 TTTATGG
1 TTTAGGG
* *
347994 ATTATGG
1 TTTAGGG
**
348001 TTTTTGG
1 TTTAGGG
348008 TTTAGGG
1 TTTAGGG
***
348015 TTTAATA
1 TTTAGGG
348022 TTTAGGG
1 TTTAGGG
*
348029 TTTAGTG
1 TTTAGGG
348036 TTTAGGG
1 TTTAGGG
* *
348043 TTTATGC
1 TTTAGGG
348050 TTTAGGG
1 TTTAGGG
**
348057 TTTAATG
1 TTTAGGG
* *
348064 TTTATGA
1 TTTAGGG
*
348071 TTTAAGG
1 TTTAGGG
* *
348078 TTTAAGT
1 TTTAGGG
* *
348085 TTTATGA
1 TTTAGGG
*
348092 TTTAAGG
1 TTTAGGG
348099 TTTAGGG
1 TTTAGGG
348106 TT
1 TT
348108 CATTGTAAAA
Statistics
Matches: 108, Mismatches: 41, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
7 108 1.00
ACGTcount: A:0.20, C:0.01, G:0.30, T:0.49
Consensus pattern (7 bp):
TTTAGGG
Found at i:348030 original size:21 final size:21
Alignment explanation
Indices: 348000--348102 Score: 91
Period size: 21 Copynumber: 4.9 Consensus size: 21
347990 ATGGATTATG
*
348000 GTTTTTGGTTTAGGGTTTAAT
1 GTTTATGGTTTAGGGTTTAAT
* * * **
348021 ATTTAGGGTTTAGTGTTTAGG
1 GTTTATGGTTTAGGGTTTAAT
*
348042 GTTTATGCTTTAGGGTTTAAT
1 GTTTATGGTTTAGGGTTTAAT
* *
348063 GTTTATGATTTAAGGTTTAA-
1 GTTTATGGTTTAGGGTTTAAT
* *
348083 GTTTTATGATTTAAGGTTTA
1 G-TTTATGGTTTAGGGTTTA
348103 GGGTTCATTG
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
20 1 0.01
21 66 0.99
ACGTcount: A:0.21, C:0.01, G:0.25, T:0.52
Consensus pattern (21 bp):
GTTTATGGTTTAGGGTTTAAT
Found at i:348067 original size:14 final size:14
Alignment explanation
Indices: 348007--348081 Score: 89
Period size: 14 Copynumber: 5.4 Consensus size: 14
347997 ATGGTTTTTG
348007 GTTTAGGGTTTAAT
1 GTTTAGGGTTTAAT
* *
348021 ATTTAGGGTTTAGT
1 GTTTAGGGTTTAAT
348035 GTTTAGGGTTT-AT
1 GTTTAGGGTTTAAT
348048 GCTTTAGGGTTTAAT
1 G-TTTAGGGTTTAAT
* * *
348063 GTTTATGATTTAAG
1 GTTTAGGGTTTAAT
348077 GTTTA
1 GTTTA
348082 AGTTTTATGA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
13 2 0.04
14 47 0.90
15 3 0.06
ACGTcount: A:0.21, C:0.01, G:0.27, T:0.51
Consensus pattern (14 bp):
GTTTAGGGTTTAAT
Found at i:348274 original size:15 final size:15
Alignment explanation
Indices: 348242--348284 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
348232 AACAACAATT
* *
348242 TTAAAAAAATAATTA
1 TTAAAAATATAATCA
*
348257 TTAAAAATATTATCA
1 TTAAAAATATAATCA
*
348272 TTAGAAATATAAT
1 TTAAAAATATAAT
348285 AAAAAATTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (15 bp):
TTAAAAATATAATCA
Found at i:352244 original size:57 final size:55
Alignment explanation
Indices: 352183--352308 Score: 170
Period size: 51 Copynumber: 2.3 Consensus size: 55
352173 TCGCAACATG
352183 AATTTCGTTTTCGAAACATTAATTACCGATATAGGTAAACACAACTATCGCAACGCA
1 AATTTCGTTTTCG-AACA-TAATTACCGATATAGGTAAACACAACTATCGCAACGCA
* *
352240 AATTTCG-TTTCG--C-TATTTACCGATATAGGTAAACACAACTATCGCAACGCG
1 AATTTCGTTTTCGAACATAATTACCGATATAGGTAAACACAACTATCGCAACGCA
*
352291 AATTTCATTTTCGCAACA
1 AATTTCGTTTTCG-AACA
352309 CGAATTTCGC
Statistics
Matches: 61, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
51 42 0.69
52 5 0.08
53 1 0.02
55 1 0.02
56 5 0.08
57 7 0.11
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (55 bp):
AATTTCGTTTTCGAACATAATTACCGATATAGGTAAACACAACTATCGCAACGCA
Found at i:352914 original size:37 final size:37
Alignment explanation
Indices: 352873--352959 Score: 167
Period size: 37 Copynumber: 2.4 Consensus size: 37
352863 TCGGTAATTA
352873 GCGTTGCGAAATTTGCATTGCGATAATTTCTATATTC
1 GCGTTGCGAAATTTGCATTGCGATAATTTCTATATTC
352910 GCGTTGCGAAATTTGCATTGCGATAATTTCTATATTC
1 GCGTTGCGAAATTTGCATTGCGATAATTTCTATATTC
352947 GCGTTGC-AAATTT
1 GCGTTGCGAAATTT
352960 AGAAACTGTG
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 6 0.12
37 44 0.88
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (37 bp):
GCGTTGCGAAATTTGCATTGCGATAATTTCTATATTC
Found at i:354253 original size:31 final size:31
Alignment explanation
Indices: 354217--354281 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
354207 TTAAAAAATA
* *
354217 TAATATTTGATCACTTTTATCTTTATTTAAT
1 TAATATTTGATCACTTTCATCTTTATATAAT
* *
354248 TAATATTTGGTCACTTTCATTTTTATATAAT
1 TAATATTTGATCACTTTCATCTTTATATAAT
354279 TAA
1 TAA
354282 GATGTGGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.09, G:0.05, T:0.55
Consensus pattern (31 bp):
TAATATTTGATCACTTTCATCTTTATATAAT
Found at i:354290 original size:31 final size:31
Alignment explanation
Indices: 354227--354293 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
354217 TAATATTTGA
* * * *
354227 TCACTTTTATCTTTATTTAATTAATATTTGG
1 TCACTTTCATCTTTATATAATTAAGATGTGG
*
354258 TCACTTTCATTTTTATATAATTAAGATGTGG
1 TCACTTTCATCTTTATATAATTAAGATGTGG
354289 TCACT
1 TCACT
354294 GAGATTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (31 bp):
TCACTTTCATCTTTATATAATTAAGATGTGG
Found at i:354446 original size:37 final size:37
Alignment explanation
Indices: 354396--354472 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
354386 AATGTTTGAG
354396 TAAGTTTTCATTTTTCCCACTAAAGTTTCAAAAGCAA
1 TAAGTTTTCATTTTTCCCACTAAAGTTTCAAAAGCAA
*
354433 TAAGTTTTCATTTTTCCCACTAAAGTTTCAAAAGTAA
1 TAAGTTTTCATTTTTCCCACTAAAGTTTCAAAAGCAA
354470 TAA
1 TAA
354473 ATTGATCAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (37 bp):
TAAGTTTTCATTTTTCCCACTAAAGTTTCAAAAGCAA
Found at i:357926 original size:2 final size:2
Alignment explanation
Indices: 357919--357979 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
357909 CCTAACTAGT
*
357919 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
357961 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
357980 GAATCTTTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:359478 original size:39 final size:38
Alignment explanation
Indices: 359434--359507 Score: 121
Period size: 39 Copynumber: 1.9 Consensus size: 38
359424 CAAAATAATA
359434 TTTTAGATATAAATAACAAATTATAATTTTTAGGAATTC
1 TTTTAGATATAAATAACAAATTAT-ATTTTTAGGAATTC
* *
359473 TTTTAGATATAAATAACCAATTATATTTTTTGGAA
1 TTTTAGATATAAATAACAAATTATATTTTTAGGAA
359508 GTTAGCAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
38 10 0.30
39 23 0.70
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (38 bp):
TTTTAGATATAAATAACAAATTATATTTTTAGGAATTC
Found at i:359744 original size:33 final size:29
Alignment explanation
Indices: 359686--359745 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 29
359676 TACATCAACT
*
359686 TTTATTAAATATATAATATATATAAAAAA
1 TTTATTAAATATATAATACATATAAAAAA
359715 TTTATTATATATATATATATACATCATAAAA
1 TTTATTA-A-ATATATA-ATACAT-ATAAAA
359746 CTCAATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 7 0.27
30 1 0.04
31 7 0.27
32 5 0.19
33 6 0.23
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (29 bp):
TTTATTAAATATATAATACATATAAAAAA
Found at i:360860 original size:33 final size:29
Alignment explanation
Indices: 360790--360870 Score: 117
Period size: 29 Copynumber: 2.7 Consensus size: 29
360780 CTTCCCAGCA
*
360790 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
360819 TAGGTCGCCATGCACTCCTGGCGACCTTGTAGG
1 TAGGTCGCCATGCACTCCTGGCGACC-T-T--G
360852 TAGGTCGCCATGCACTCCT
1 TAGGTCGCCATGCACTCCT
360871 CCTGCTCCTC
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
29 25 0.53
30 1 0.02
31 1 0.02
33 20 0.43
ACGTcount: A:0.15, C:0.33, G:0.28, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCTGGCGACCTTG
Found at i:360963 original size:14 final size:14
Alignment explanation
Indices: 360926--360963 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
360916 GCTCACTCGA
360926 ATGGCCTCGGTCGG
1 ATGGCCTCGGTCGG
*
360940 ATGCCCTCGGTCGG
1 ATGGCCTCGGTCGG
*
360954 ATGGCTTCGG
1 ATGGCCTCGG
360964 ATGCCCAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.08, C:0.29, G:0.39, T:0.24
Consensus pattern (14 bp):
ATGGCCTCGGTCGG
Found at i:363374 original size:20 final size:19
Alignment explanation
Indices: 363327--363374 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
363317 CTAAAACGAA
*
363327 ATAATATAAATATCACAACC
1 ATAATAT-AATATCACAAAC
363347 A-AATTATAATATCAGCAAAC
1 ATAA-TATAATATCA-CAAAC
363367 ATAATATA
1 ATAATATA
363375 CAAATTAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 9 0.38
20 13 0.54
21 2 0.08
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.27
Consensus pattern (19 bp):
ATAATATAATATCACAAAC
Found at i:364552 original size:3 final size:3
Alignment explanation
Indices: 364544--364605 Score: 72
Period size: 3 Copynumber: 19.3 Consensus size: 3
364534 ATTAATAAAC
364544 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATAA ATA ATA ATA A-A TATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA -ATA
364591 TATAA ATA ATA ATA A
1 -AT-A ATA ATA ATA A
364606 AAAAGACCCG
Statistics
Matches: 54, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 1 0.02
3 40 0.74
4 12 0.22
5 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:364559 original size:19 final size:19
Alignment explanation
Indices: 364544--364605 Score: 99
Period size: 19 Copynumber: 3.2 Consensus size: 19
364534 ATTAATAAAC
364544 ATAATAATAATAAATAATA
1 ATAATAATAATAAATAATA
364563 ATAATAATAATAAATAATA
1 ATAATAATAATAAATAATA
364582 ATAA-ATATATATAAATAATA
1 ATAATA-ATA-ATAAATAATA
364602 ATAA
1 ATAA
364606 AAAAGACCCG
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
18 1 0.02
19 26 0.63
20 14 0.34
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAATAATAATAAATAATA
Found at i:364561 original size:10 final size:10
Alignment explanation
Indices: 364546--364606 Score: 99
Period size: 10 Copynumber: 6.2 Consensus size: 10
364536 TAATAAACAT
364546 AATAATAATA
1 AATAATAATA
364556 AATAATAAT-
1 AATAATAATA
364565 AATAATAATA
1 AATAATAATA
364575 AATAATAATA
1 AATAATAATA
364585 AAT-ATATATA
1 AATAATA-ATA
364595 AATAATAATA
1 AATAATAATA
364605 AA
1 AA
364607 AAAGACCCGG
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
9 12 0.25
10 33 0.69
11 3 0.06
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AATAATAATA
Found at i:364563 original size:16 final size:16
Alignment explanation
Indices: 364544--364606 Score: 76
Period size: 16 Copynumber: 3.9 Consensus size: 16
364534 ATTAATAAAC
364544 ATAATAATAATAAATA
1 ATAATAATAATAAATA
364560 ATAATAATAAT-AATAA
1 ATAATAATAATAAAT-A
*
364576 ATAATAATAA-ATATA
1 ATAATAATAATAAATA
364591 TATAAATAATAATAAA
1 -AT-AATAATAATAAA
364607 AAAGACCCGG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 4 0.10
16 26 0.65
17 8 0.20
18 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAATAATAATAAATA
Found at i:364895 original size:46 final size:44
Alignment explanation
Indices: 364835--365068 Score: 175
Period size: 46 Copynumber: 5.4 Consensus size: 44
364825 TCGGGGAATG
*
364835 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAAGAG-TCTGGCCATCT-AAGGTGATA
* * * ** * *
364881 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT--TG
1 ACACGGCTCCTACGTGATGAAGA-GTCTGGCCATCTAAGGTGATA
*
364924 ACACGGCTCCTACGTGATGAAGA-TCTGG---TCT--GG-GAATG
1 ACACGGCTCCTACGTGATGAAGAGTCTGGCCATCTAAGGTG-ATA
*
364962 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAAGAG-TCTGGCCATCT-AAGGTGATA
* * * ** * *
365008 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT--TG
1 ACACGGCTCCTACGTGATGAAGA-GTCTGGCCATCTAAGGTGATA
365051 ACACGGCTCCTACGTGAT
1 ACACGGCTCCTACGTGAT
365069 AAGGAAATCT
Statistics
Matches: 152, Mismatches: 22, Indels: 31
0.74 0.11 0.15
Matches are distributed among these distances:
36 2 0.01
38 27 0.18
40 5 0.03
41 4 0.03
43 43 0.28
45 8 0.05
46 60 0.39
47 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (44 bp):
ACACGGCTCCTACGTGATGAAGAGTCTGGCCATCTAAGGTGATA
Found at i:364939 original size:43 final size:41
Alignment explanation
Indices: 364881--365120 Score: 159
Period size: 43 Copynumber: 5.7 Consensus size: 41
364871 AAAGGTGATA
* *
364881 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGACGGCTGG--ATCTAGGGTTG
* * *
364924 ACACGGCTCCTACGTGATGAAGA--TCTGG-TCT-GGGAATG
1 ACACGGCTCCTACGTGATGAGGACGGCTGGATCTAGGG-TTG
* * * * *
364962 ACACGGCTCATACGTGATGAAGA-GTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGACG-GCTGG--ATCT--AGG-GTTG
* *
365008 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGACGGCTGG--ATCTAGGGTTG
* *** * *
365051 ACACGGCTCCTACGTGATAAGGAAATCTGG-TCTGGGGATG
1 ACACGGCTCCTACGTGATGAGGACGGCTGGATCTAGGGTTG
* *
365091 ACACGGTTCCTACATGATGAGGACGGCTGG
1 ACACGGCTCCTACGTGATGAGGACGGCTGG
365121 CCATCTTTAG
Statistics
Matches: 156, Mismatches: 30, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
37 2 0.01
38 27 0.17
40 36 0.23
41 4 0.03
43 51 0.33
44 2 0.01
46 32 0.21
47 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.25
Consensus pattern (41 bp):
ACACGGCTCCTACGTGATGAGGACGGCTGGATCTAGGGTTG
Found at i:365045 original size:127 final size:127
Alignment explanation
Indices: 364802--365110 Score: 512
Period size: 127 Copynumber: 2.4 Consensus size: 127
364792 TTAACGCGGT
* *
364802 TCCTACGTGATGAGGACATCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
1 TCCTACGTGATGA--AGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
364867 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
64 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
364931 TCCTACGTGATGAAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCAT
1 TCCTACGTGATGAAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCAT
364996 CTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
66 CTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
* * * *
365058 TCCTACGTGAT-AAGGAAATCTGGTCTGGGGATGACACGGTTCCTACATGATGA
1 TCCTACGTGATGAA-G--ATCTGGTCTGGGAATGACACGGCTCATACGTGATGA
365111 GGACGGCTGG
Statistics
Matches: 171, Mismatches: 6, Indels: 6
0.93 0.03 0.03
Matches are distributed among these distances:
126 2 0.01
127 124 0.73
129 45 0.26
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.26
Consensus pattern (127 bp):
TCCTACGTGATGAAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCAT
CTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
Found at i:365463 original size:66 final size:63
Alignment explanation
Indices: 365274--365456 Score: 161
Period size: 66 Copynumber: 2.8 Consensus size: 63
365264 TTTCAAAAGC
* ** * *
365274 AACTGTCTCGAAAGAGACAAAATTCGTTTCAAATGAAAC-AACTCAAAAGATGACGTTTAAAGGG
1 AACTGTCTC-AAAGAGACAAAATTCATTTCAAGGGAAACGATCTC-AAAGATGATGTTTAAAGGG
* * ** * * * * * *
365338 AATTGTCTCAAGCGAGACAAAATTTGTTTTTAAGGGAAACGTTCTCAAATATCGGTGTTTCATGG
1 AACTGTCTCAA-AGAGACAAAA-TTCATTTCAAGGGAAACGATCTCAAAGAT-GATGTTTAAAGG
365403 G
63 G
365404 AAACTGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
1 -AACTGTCTCAAA-GAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
365457 TTTGTTTTGT
Statistics
Matches: 92, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
63 2 0.02
64 17 0.18
65 18 0.20
66 36 0.39
67 19 0.21
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (63 bp):
AACTGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGATGTTTAAAGGG
Found at i:365861 original size:31 final size:30
Alignment explanation
Indices: 365797--365871 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
365787 ATAGAAAATG
*
365797 TTTCAAGTGAAACGACTCAAAAATGGTTTTA
1 TTTCAAGTGAAACAACTCAAAAAT-GTTTTA
*
365828 TTTCAAGTGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGTGAAAC-AACTCAAAAATGTTT-TA
* *
365859 TTTCTAGAGAAAC
1 TTTCAAGTGAAAC
365872 TGCCTCAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 26 0.68
32 9 0.24
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (30 bp):
TTTCAAGTGAAACAACTCAAAAATGTTTTA
Found at i:365964 original size:40 final size:40
Alignment explanation
Indices: 365904--365983 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
365894 GTTTTAATAA
365904 AAACAATCTCAAAGGTGGGTAGTTTT-AAAAGAAATTGTCT
1 AAACAATCTCAAAGGTGGGTA-TTTTCAAAAGAAATTGTCT
* * *
365944 AAACGATCTCAAATGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
365984 CGAGAGACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (40 bp):
AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
Found at i:366038 original size:63 final size:64
Alignment explanation
Indices: 365965--366089 Score: 189
Period size: 64 Copynumber: 2.0 Consensus size: 64
365955 AATGTGGGTA
* * *
365965 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
* * *
366028 TTTTCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
366090 GGATCACATC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
63 17 0.31
64 38 0.69
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (64 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
Found at i:366202 original size:120 final size:119
Alignment explanation
Indices: 365987--366210 Score: 276
Period size: 120 Copynumber: 1.9 Consensus size: 119
365977 GTTGTCTCGA
* *
365987 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTAAG
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTTCAAG
*
366052 AGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCACATCTTAAGT
66 AGAGAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCACATCTTAAGT
* * * **
366106 GAGACCAAA-TTTGTTTCAAATGAAACAATCTCAAA-AGTTAGTTTTTCATTAGAAACTGTC-TC
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGA-TT--TTTTTCAAAAGAAACTGTCTTC
** *
366168 AAGAGAGACAACA-TTTGTTTTTAAAGAAATAGACTCAAAGATG
63 AAGAGAGA-AA-ATTTTGTTTCAAAAGAAACAGACTCAAAGATG
366211 ATTTTGTTAA
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
117 1 0.01
118 26 0.29
119 16 0.18
120 45 0.51
121 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (119 bp):
GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTTCAAG
AGAGAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCACATCTTAAGT
Found at i:366378 original size:37 final size:37
Alignment explanation
Indices: 366322--366448 Score: 117
Period size: 37 Copynumber: 3.6 Consensus size: 37
366312 GAAACAGATT
*
366322 CAAAGATTTT-TTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAA-ATTTTGTTTCAAAAGAAACTATCTTAAGAGAGA
* * * *
366359 CAAAATTTTGTTTCCAAAGAAACAAAC-TCA-A-AG-
1 CAAAATTTTGTTTCAAAAGAAACTATCTTAAGAGAGA
* *
366392 ---ATTTTTGTTTTAAAAGAAACTATCTTAAGAGAGA
1 CAAAATTTTGTTTCAAAAGAAACTATCTTAAGAGAGA
*
366426 CAAAATTTTGTTTCCAAAGAAAC
1 CAAAATTTTGTTTCAAAAGAAAC
366449 AAACTCAAAG
Statistics
Matches: 68, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
30 19 0.28
31 2 0.03
32 1 0.01
33 2 0.03
34 2 0.03
35 1 0.01
36 7 0.10
37 34 0.50
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAAAGAAACTATCTTAAGAGAGA
Found at i:366422 original size:67 final size:66
Alignment explanation
Indices: 366269--366480 Score: 265
Period size: 67 Copynumber: 3.3 Consensus size: 66
366259 AAAGATTTAC
* * * * * * *
366269 TTCAAGAGAAACTGTCTCAAGAGATACAAAATTCAT-TTT--AAGAGAAACAGATTCAAAGA-TT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATT-TTGTTTCCAA-AGAAACAAACTCAAAGATTT
366330 TTT
64 TTT
*
366333 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
366398 GT
66 -T
*
366400 TTTAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGA--TTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
366463 T
66 T
*
366464 TTCAAAAGAAACAATCT
1 TTCAAAAGAAACTATCT
366481 CAAAGATTTT
Statistics
Matches: 131, Mismatches: 12, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 47 0.36
65 18 0.14
66 6 0.05
67 59 0.45
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.30
Consensus pattern (66 bp):
TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
T
Found at i:366490 original size:26 final size:27
Alignment explanation
Indices: 366436--366492 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
366426 CAAAATTTTG
*
366436 TTTCCAAAGAAACAAACTCAAAGATTT
1 TTTCAAAAGAAACAAACTCAAAGATTT
*
366463 TTTCAAAAGAAACAATCTCAAAGATTT
1 TTTCAAAAGAAACAAACTCAAAGATTT
366490 TTT
1 TTT
366493 TTCACAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.32
Consensus pattern (27 bp):
TTTCAAAAGAAACAAACTCAAAGATTT
Found at i:366684 original size:83 final size:82
Alignment explanation
Indices: 366594--366749 Score: 217
Period size: 83 Copynumber: 1.9 Consensus size: 82
366584 AAATAAATAG
* *
366594 ACTCAAAGA-TTTTTCAAAAGAAAC-AACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGA
1 ACTCAAAGATTTTTTCAAAAGAAACAAACTCAAAGAT-TTT-TTCAAAAGAAACAAACTCAAAGA
366657 GTTTTATTCAAAAGGAGCAA
64 -TTTTATTCAAAAGGAGCAA
* * *
366677 ACTCAAAGATTTTTTCAAGAGGAACAAACTCAAAGATTTTTTCAAGAGAAACAAACTCAAAGATT
1 ACTCAAAGATTTTTTCAAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAACAAACTCAAAGATT
*
366742 TTTTTCAA
66 TTATTCAA
366750 GAGAAACTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
82 9 0.14
83 29 0.45
84 16 0.25
85 11 0.17
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (82 bp):
ACTCAAAGATTTTTTCAAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAACAAACTCAAAGATT
TTATTCAAAAGGAGCAA
Found at i:366704 original size:27 final size:27
Alignment explanation
Indices: 366594--366745 Score: 200
Period size: 27 Copynumber: 5.6 Consensus size: 27
366584 AAATAAATAG
*
366594 ACTCAAAGA-TTTTTCAAAAGAAAC-A
1 ACTCAAAGATTTTTTCAAAAGGAACAA
366619 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGAT-TTT-TTCAAAAGGAACAA
* *
366648 ACTCCAAGAGTTTTATTCAAAAGGAGCAA
1 ACTCAAAGA-TTTT-TTCAAAAGGAACAA
*
366677 ACTCAAAGATTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTTCAAAAGGAACAA
* *
366704 ACTCAAAGATTTTTTCAAGAGAAACAA
1 ACTCAAAGATTTTTTCAAAAGGAACAA
366731 ACTCAAAGATTTTTT
1 ACTCAAAGATTTTTT
366746 TCAAGAGAAA
Statistics
Matches: 115, Mismatches: 7, Indels: 8
0.88 0.05 0.06
Matches are distributed among these distances:
25 9 0.08
27 56 0.49
28 15 0.13
29 34 0.30
30 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (27 bp):
ACTCAAAGATTTTTTCAAAAGGAACAA
Found at i:366753 original size:28 final size:27
Alignment explanation
Indices: 366579--366756 Score: 198
Period size: 27 Copynumber: 6.5 Consensus size: 27
366569 CAAAACTTTG
* * *
366579 TTTCAAAATAAATAGACTCAAAGA-TT
1 TTTCAAAAGAAACAAACTCAAAGATTT
366605 TTTCAAAAGAAAC-AACTCAAAGATATT
1 TTTCAAAAGAAACAAACTCAAAGAT-TT
* *
366632 TATTCAAAAGGAACAAACTCCAAGAGTTT
1 T-TTCAAAAGAAACAAACTCAAAGA-TTT
* *
366661 TATTCAAAAGGAGCAAACTCAAAGATTT
1 T-TTCAAAAGAAACAAACTCAAAGATTT
* *
366689 TTTCAAGAGGAACAAACTCAAAGATTT
1 TTTCAAAAGAAACAAACTCAAAGATTT
*
366716 TTTCAAGAGAAACAAACTCAAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGA-TTT
*
366744 TTTCAAGAGAAAC
1 TTTCAAAAGAAAC
366757 TGTCTCAAGA
Statistics
Matches: 136, Mismatches: 10, Indels: 10
0.87 0.06 0.06
Matches are distributed among these distances:
25 9 0.07
26 11 0.08
27 50 0.37
28 31 0.23
29 34 0.25
30 1 0.01
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (27 bp):
TTTCAAAAGAAACAAACTCAAAGATTT
Found at i:367082 original size:36 final size:35
Alignment explanation
Indices: 366998--367095 Score: 117
Period size: 36 Copynumber: 2.8 Consensus size: 35
366988 GAGAAAATGA
* *
366998 TGTCTCAAGCGAGACAAAATTTG-CTTTAAGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
* **
367032 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTA-AGAAAT
* *
367068 TGTCTCAAGCGAGACACAGTTTGTTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT
367096 GAGGAAACGA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 20 0.38
35 4 0.08
36 28 0.54
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
Found at i:367315 original size:36 final size:36
Alignment explanation
Indices: 367275--367356 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
367265 AAAGGAAAAA
* * *
367275 TGTCTCAAGCGAGACGAAGTTTG-TTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAACTTTGTTTTTAA-AGAAAT
* * *
367311 TGTCTTAAGTGATACAAACTTTGTTTTTAAAGAAAT
1 TGTCTCAAGCGAGACAAACTTTGTTTTTAAAGAAAT
367347 TGTCTCAAGC
1 TGTCTCAAGC
367357 AAAACAAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
36 31 0.84
37 6 0.16
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAACTTTGTTTTTAAAGAAAT
Found at i:367364 original size:36 final size:36
Alignment explanation
Indices: 367275--367369 Score: 93
Period size: 36 Copynumber: 2.6 Consensus size: 36
367265 AAAGGAAAAA
* * * *
367275 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAAACAAAATTTGTTTTAAGAGAAAT
* * * *
367311 TGTCTTAAGTGATACAAACTTTGTTTTTAA-AGAAAT
1 TGTCTCAAGCGAAACAAAATTTG-TTTTAAGAGAAAT
*
367347 TGTCTCAAGCAAAACAAAATTTG
1 TGTCTCAAGCGAAACAAAATTTG
367370 AGAAAACGAT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
36 41 0.87
37 6 0.13
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.35
Consensus pattern (36 bp):
TGTCTCAAGCGAAACAAAATTTGTTTTAAGAGAAAT
Found at i:367499 original size:36 final size:35
Alignment explanation
Indices: 367459--367576 Score: 148
Period size: 36 Copynumber: 3.3 Consensus size: 35
367449 AGTGAGGCGG
367459 AATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAA
1 AATTTGTTTTT-AAGAAATTGTCTCAAACGAGACAA
* *
367495 AATTTGTTTTT-AGAAAGCTGTCTCAATCGAGACAA
1 AATTTGTTTTTAAGAAA-TTGTCTCAAACGAGACAA
** *
367530 AATTTGCTTTGAAAGAAATTGTCTCAAGCGAGACAAA
1 AATTTG-TTTTTAAGAAATTGTCTCAAACGAGAC-AA
367567 AATTTGTTTT
1 AATTTGTTTT
367577 AAAATTCTCA
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
34 5 0.07
35 22 0.31
36 31 0.44
37 13 0.18
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (35 bp):
AATTTGTTTTTAAGAAATTGTCTCAAACGAGACAA
Found at i:368141 original size:14 final size:14
Alignment explanation
Indices: 368122--368149 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
368112 TTTATGTATC
368122 ATGTATGTATGTGT
1 ATGTATGTATGTGT
368136 ATGTATGTATGTGT
1 ATGTATGTATGTGT
368150 TCTCAATCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (14 bp):
ATGTATGTATGTGT
Found at i:371217 original size:31 final size:32
Alignment explanation
Indices: 371158--371219 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
371148 TGACAAAATG
*
371158 ACACAAACAAAAGAGAAGAAATATGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
371190 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
371220 CATGTAGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 12 0.41
32 17 0.59
ACGTcount: A:0.60, C:0.10, G:0.15, T:0.16
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:375336 original size:3 final size:3
Alignment explanation
Indices: 375328--375388 Score: 79
Period size: 3 Copynumber: 19.3 Consensus size: 3
375318 ATTAATAAAC
375328 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA A-A TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA -ATA
375374 TATAA ATA ATA ATA A
1 -AT-A ATA ATA ATA A
375389 AAAAGACTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
2 1 0.02
3 43 0.80
4 9 0.17
5 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:380523 original size:17 final size:18
Alignment explanation
Indices: 380498--380542 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
380488 AGTATTTCAT
380498 TTTAGAAATTATTTTTA-A
1 TTTA-AAATTATTTTTAGA
380516 TTTAAAA-TATTTTTAGA
1 TTTAAAATTATTTTTAGA
*
380533 GTTAAAATTA
1 TTTAAAATTA
380543 ATATTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 8 0.33
17 10 0.42
18 6 0.25
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (18 bp):
TTTAAAATTATTTTTAGA
Found at i:380528 original size:16 final size:17
Alignment explanation
Indices: 380507--380540 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
380497 TTTTAGAAAT
*
380507 TATTTTTA-ATTTAAAA
1 TATTTTTAGAGTTAAAA
380523 TATTTTTAGAGTTAAAA
1 TATTTTTAGAGTTAAAA
380540 T
1 T
380541 TAATATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TATTTTTAGAGTTAAAA
Found at i:388876 original size:9 final size:10
Alignment explanation
Indices: 388841--388873 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
388831 TTTGAATTAT
388841 TTTTGAAAAC
1 TTTTGAAAAC
388851 TTTTGAAAAC
1 TTTTGAAAAC
388861 TTTTGAAAAC
1 TTTTGAAAAC
388871 TTT
1 TTT
388874 GAACAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (10 bp):
TTTTGAAAAC
Found at i:393294 original size:23 final size:23
Alignment explanation
Indices: 393268--393313 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
393258 CACCACAACT
* *
393268 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTACACCGAAGTGCCA
*
393291 CGTAGAATTACACCGGAGTGCCA
1 CGTAGAATTACACCGAAGTGCCA
393314 TATAATAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAATTACACCGAAGTGCCA
Found at i:397576 original size:204 final size:204
Alignment explanation
Indices: 397226--397639 Score: 774
Period size: 204 Copynumber: 2.0 Consensus size: 204
397216 CTTAAAGGCT
* **
397226 CAAATCTCACCAAATTGTTTCATGCATTGAGCTAATCACATTTCAACCAATAAAACCATGGAATA
1 CAAATCTCACCAAATTATTTCATGCATCAAGCTAATCACATTTCAACCAATAAAACCATGGAATA
397291 TCACAAAAGTACCAACTTGATCACAATTCATGCTATTCGCTATCAAGAATATCCTAACCTAAACA
66 TCACAAAAGTACCAACTTGATCACAATTCATGCTATTCGCTATCAAGAATATCCTAACCTAAACA
397356 ATCATGTGTTCCCAAACAAACATAGCATTCCAAACAATATTCAACAAGACAAAGACAATCAATGA
131 ATCATGTGTTCCCAAACAAACATAGCATTCCAAACAATATTCAACAAGACAAAGACAATCAATGA
397421 AATTTTTGA
196 AATTTTTGA
* *
397430 CAAATCTCACCAAATTATTTCATGCATCAAGCTAATCACATTTCAATCAATAAAACCATGGGATA
1 CAAATCTCACCAAATTATTTCATGCATCAAGCTAATCACATTTCAACCAATAAAACCATGGAATA
397495 TCACAAAAGTACCAACTTGATCACAATTCATGCTATTCGCTATCAAGAATATCCTAACCTAAACA
66 TCACAAAAGTACCAACTTGATCACAATTCATGCTATTCGCTATCAAGAATATCCTAACCTAAACA
*
397560 ATCATGTGTTCCCAAACAAGCATAGCATTCCAAACAATATTCAACAAGACAAAGACAATCAATGA
131 ATCATGTGTTCCCAAACAAACATAGCATTCCAAACAATATTCAACAAGACAAAGACAATCAATGA
397625 AATTTTTGA
196 AATTTTTGA
397634 CAAATC
1 CAAATC
397640 CAACCAACAC
Statistics
Matches: 204, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
204 204 1.00
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (204 bp):
CAAATCTCACCAAATTATTTCATGCATCAAGCTAATCACATTTCAACCAATAAAACCATGGAATA
TCACAAAAGTACCAACTTGATCACAATTCATGCTATTCGCTATCAAGAATATCCTAACCTAAACA
ATCATGTGTTCCCAAACAAACATAGCATTCCAAACAATATTCAACAAGACAAAGACAATCAATGA
AATTTTTGA
Found at i:413201 original size:3 final size:3
Alignment explanation
Indices: 413193--413253 Score: 95
Period size: 3 Copynumber: 20.0 Consensus size: 3
413183 TTATTTATTA
* *
413193 AAT AAT AAT AAT ATAT AAT ATT AAT ATT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
413239 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
413254 CAAATGAATC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:413641 original size:84 final size:83
Alignment explanation
Indices: 413501--413693 Score: 278
Period size: 84 Copynumber: 2.3 Consensus size: 83
413491 CTTTCAGATG
* * *
413501 AGTTCTTCTCATTATGAACATTTCTGGAAATGTTGATGTTGATCCATCTACTTCTGTGATAGAGT
1 AGTTCTTCTCATTATGAACTTTTCTGGAAAAGTTGATGTTGATCCATCTAATTCTGTGATAGAGT
*
413566 TAAACAAAAGGTTAAACA
66 CAAACAAAAGGTTAAACA
*
413584 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTAATTCTGTGATAGAG
1 AGTTCTTCTCATTATGAACTTT-TCTGGAAAAGTTGATGTTGATCCATCTAATTCTGTGATAGAG
** *
413649 TCATGCAAAAGGTTGAACA
65 TCAAACAAAAGGTTAAACA
**
413668 AACTCTTCTCATTATGAACTTCTTCT
1 AGTTCTTCTCATTATGAACTT-TTCT
413694 TCATTCTTCA
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
83 21 0.21
84 76 0.78
85 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (83 bp):
AGTTCTTCTCATTATGAACTTTTCTGGAAAAGTTGATGTTGATCCATCTAATTCTGTGATAGAGT
CAAACAAAAGGTTAAACA
Found at i:414019 original size:224 final size:224
Alignment explanation
Indices: 413758--414352 Score: 1091
Period size: 224 Copynumber: 2.6 Consensus size: 224
413748 TGATTAAACT
*
413758 AAAGTCGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
413823 TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGCAAAAGGTTGAACAAATTCTTC
66 TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGCAAAAGGTTGAACAAATTCTTC
*
413888 TCATTATGAATTTCTCATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGATAATA
131 TCATTATGAATTTCTCATTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCTACCTGATAATA
413953 CTGAATCATCGAATGATGAATTCAAGCGA
196 CTGAATCATCGAATGATGAATTCAAGCGA
*
413982 AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTTTTCTCATTA
1 AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
*
414047 TGAACTTTTTCTGGAAAAGCAGATCCATCAAGTGATGGATTTGCAAAAGGTTGAACAAATTCTTC
66 TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGCAAAAGGTTGAACAAATTCTTC
* *
414112 TCATTATGAATTTCTCCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCTACCTGGTAATA
131 TCATTATGAATTTCTCATTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCTACCTGATAATA
414177 CTGAATCATCGAATGATGAATTCAAGCGA
196 CTGAATCATCGAATGATGAATTCAAGCGA
* *
414206 AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTATTCTTTCTTCAAATGAGTTCTTCTCATTA
1 AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
414271 TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCT
66 TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTT--GCAAAAGGTTGAACAAATTCT
*
414336 TCTCATTATGAACTTCT
129 TCTCATTATGAATTTCT
414353 TCAGATAAAT
Statistics
Matches: 358, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
224 321 0.90
226 37 0.10
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (224 bp):
AAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGCAAAAGGTTGAACAAATTCTTC
TCATTATGAATTTCTCATTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCTACCTGATAATA
CTGAATCATCGAATGATGAATTCAAGCGA
Found at i:414031 original size:113 final size:111
Alignment explanation
Indices: 413764--414354 Score: 779
Period size: 113 Copynumber: 5.3 Consensus size: 111
413754 AACTAAAGTC
413764 GAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
*
413829 TTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGCAAAAGGTT
66 TTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTAGCAAAAGGTT
* *
413875 GAACAAATTCTTCTCATTATGAATTTC-TCATTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 GAACAAATTCTTCTCATTATGAACTTCTTC-TTCTTTCTTCAGATGAGTTCTTCTCATTATGAAC
* ** *
413939 TCTACCT-GATAATA-CTGAAT-CATCGAA-TGATGAATTCAAGCGAAAA-GTT
65 TTTTTCTGGA-AA-AGCTG-ATCCATC-AAGTGATGGATT--AGC-AAAAGGTT
*
413988 GAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTTTTCTCATTATGAACT
1 GAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
* *
414053 TTTTCTGGAAAAGCAGATCCATCAAGTGATGGATTTGCAAAAGGTT
66 TTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTAGCAAAAGGTT
* * * *
414099 GAACAAATTCTTCTCATTATGAATTTCTCCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACT
1 GAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
* ** * *
414164 CTACCTGGTAATA-CTGAAT-CATCGAA-TGATGAATTCAAGCGAAAA-GTT
66 TTTTCTGG-AAAAGCTG-ATCCATC-AAGTGATGGATT--AGC-AAAAGGTT
* *
414212 GAACAAATTCTTCTCATTATGAACTTCTTATTCTTTCTTCAAATGAGTTCTTCTCATTATGAACT
1 GAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
414277 TTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTT
66 TTTTCTGGAAAAGCTGATCCATCAAGTGATGGA-TT-AGCAAAAGGTT
414325 GAACAAATTCTTCTCATTATGAACTTCTTC
1 GAACAAATTCTTCTCATTATGAACTTCTTC
414355 AGATAAATTC
Statistics
Matches: 414, Mismatches: 41, Indels: 48
0.82 0.08 0.10
Matches are distributed among these distances:
110 8 0.02
111 164 0.40
112 28 0.07
113 200 0.48
114 14 0.03
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (111 bp):
GAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
TTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTAGCAAAAGGTT
Found at i:414745 original size:123 final size:123
Alignment explanation
Indices: 414449--414889 Score: 450
Period size: 124 Copynumber: 3.7 Consensus size: 123
414439 GAATCAATGC
* *
414449 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * * *
414514 GAAC-TTCACCTGGAAATAGCTCTGCTGCTCTATCTCTTTTTGGAAATGGAATCAAGCAA
66 GAACTTTC-TCTGGAAATAGCTCTGCTGATCTATCTCCTTCTGG-AATAGAATCAAGCAA
* *
414573 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTCAGATAAGCTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * * *
414638 GAACTTTCTCTGGAAA-AGTTGGTGTTGATCTATCTCCTTCTGTG-ATAGATTCATGCAA
66 GAACTTTCTCTGGAAATAGCT-CTGCTGATCTATCTCCTTCTG-GAATAGAATCAAGCAA
* *
414696 AAGGTTGAACAAGCTT-TTCTCATTATGAACTTCTTCTTACTCTTCAGATAAATTCTTCTCATTA
1 AAGGTTGAACAAG-TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
* * *** **
414760 TGAACTTTCTCTGG-CA-A---C-GCTGATCCA--T-CGGGT-G-AT-GAATTTGAGCAA
65 TGAACTTTCTCTGGAAATAGCTCTGCTGATCTATCTCCTTCTGGAATAGAA-TCAAGCAA
* * *
414808 AATGTTGAACAAGTTCTTCTCATTATGAACTT-TTCCTTCCTCTTCAAATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTT-CTTCCTCTTCAGATAAGTTCTTCTCATTA
*
414872 TGAACTCT-TCTGGAAATA
65 TGAACTTTCTCTGGAAATA
414890 TTGAAAACAT
Statistics
Matches: 272, Mismatches: 36, Indels: 29
0.81 0.11 0.09
Matches are distributed among these distances:
111 11 0.04
112 69 0.25
113 1 0.00
114 2 0.01
115 1 0.00
117 7 0.03
122 2 0.01
123 85 0.31
124 90 0.33
125 4 0.01
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.39
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
GAACTTTCTCTGGAAATAGCTCTGCTGATCTATCTCCTTCTGGAATAGAATCAAGCAA
Found at i:415718 original size:19 final size:19
Alignment explanation
Indices: 415694--415733 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
415684 CTTGGATAAA
415694 ACCAACTTTATTTGTTTGG
1 ACCAACTTTATTTGTTTGG
415713 ACCAACTTTATTTGTTTGG
1 ACCAACTTTATTTGTTTGG
415732 AC
1 AC
415734 TTGTGTAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (19 bp):
ACCAACTTTATTTGTTTGG
Found at i:415783 original size:22 final size:22
Alignment explanation
Indices: 415758--415812 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
415748 CATAAAGTTT
*
415758 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
415780 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
415802 TCATCTTTGAA
1 TCATCTTTGAA
415813 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:416322 original size:54 final size:54
Alignment explanation
Indices: 416237--416374 Score: 197
Period size: 54 Copynumber: 2.6 Consensus size: 54
416227 CGAGATGTAA
* * *
416237 AACACTTTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTTGGAAAACATTTGAC
1 AACACATTCATCCTTTTCTGTGGCTTCTGCTCAGACGTTTAGAAAACATTTGAC
* * * *
416291 AACACATTCATCC-TTTCTTGTGGTTTTTGCTCAGACGTTTATAAAGCATTTGAC
1 AACACATTCATCCTTTTC-TGTGGCTTCTGCTCAGACGTTTAGAAAACATTTGAC
416345 AACACATTCATCCTTTTCTGTGGCTTCTGC
1 AACACATTCATCCTTTTCTGTGGCTTCTGC
416375 CAAGATTTCT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
53 4 0.05
54 65 0.89
55 4 0.05
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (54 bp):
AACACATTCATCCTTTTCTGTGGCTTCTGCTCAGACGTTTAGAAAACATTTGAC
Found at i:425758 original size:16 final size:15
Alignment explanation
Indices: 425723--425777 Score: 69
Period size: 16 Copynumber: 3.7 Consensus size: 15
425713 ATTCTTGAAT
*
425723 ATAATAAATA-AATA
1 ATAATAAAAATAATA
425737 A-AATAAAAATAATA
1 ATAATAAAAATAATA
425751 ATATATAAAAATAATA
1 ATA-ATAAAAATAATA
425767 AGTAATAAAAA
1 A-TAATAAAAA
425778 AATTGAAAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
13 7 0.19
14 6 0.17
15 1 0.03
16 20 0.56
17 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (15 bp):
ATAATAAAAATAATA
Found at i:427897 original size:3 final size:3
Alignment explanation
Indices: 427889--427958 Score: 113
Period size: 3 Copynumber: 23.0 Consensus size: 3
427879 TTATTTATTA
* *
427889 AAT AAT AAT AAT ATAT AAT ATT AAT ATT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
427935 AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
427959 CAAATGAATC
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 59 0.95
4 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:434779 original size:36 final size:35
Alignment explanation
Indices: 434651--434771 Score: 102
Period size: 35 Copynumber: 3.4 Consensus size: 35
434641 TCTTAGGTCC
* *
434651 ATAAGGAATTACCAACTCGATCGGT-CTGAACCTAT
1 ATAAGAAATTACCAACT-GATCGGTGATGAACCTAT
**** **
434686 ATAAGAAATTAACGGTTTGATCGAAGATGAACCTGCA-
1 ATAAGAAATT-ACCAACTGATCGGTGATGAACCT--AT
*
434723 ATAAGAAATTACCAACTGATCGGTGTTGAACCTAT
1 ATAAGAAATTACCAACTGATCGGTGATGAACCTAT
*
434758 ATAAGGAATTACCA
1 ATAAGAAATTACCA
434772 GCCTGATCAG
Statistics
Matches: 65, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
34 1 0.02
35 27 0.42
36 26 0.40
37 10 0.15
38 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (35 bp):
ATAAGAAATTACCAACTGATCGGTGATGAACCTAT
Found at i:434779 original size:72 final size:72
Alignment explanation
Indices: 434651--434792 Score: 180
Period size: 72 Copynumber: 2.0 Consensus size: 72
434641 TCTTAGGTCC
* * **
434651 ATAAGGAATTACCAACTCGATCGGTCTGAACCTATATAAGAAATTAACGGTTTGATCGAAGA-TG
1 ATAAGAAATTACCAACTCGATCGGTCTGAACCTATATAAGAAATTAACAGCCTGATC-AAGACTG
434715 AACCTGCA
65 AACCTGCA
* * * *
434723 ATAAGAAATTACCAACT-GATCGGTGTTGAACCTATATAAGGAATTACCAGCCTGATCAGGACTG
1 ATAAGAAATTACCAACTCGATCGGT-CTGAACCTATATAAGAAATTAACAGCCTGATCAAGACTG
434787 AACCTG
65 AACCTG
434793 TAGAGACTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
71 10 0.17
72 50 0.83
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.25
Consensus pattern (72 bp):
ATAAGAAATTACCAACTCGATCGGTCTGAACCTATATAAGAAATTAACAGCCTGATCAAGACTGA
ACCTGCA
Found at i:434789 original size:36 final size:34
Alignment explanation
Indices: 434651--434791 Score: 97
Period size: 36 Copynumber: 3.9 Consensus size: 34
434641 TCTTAGGTCC
* *
434651 ATAAGGAATTACCAACTCGATCGGTCTGAACCTAT
1 ATAAGAAATTACCAACT-GATCGGACTGAACCTAT
****
434686 ATAAGAAATTAACGGTTTGATCGAAGA-TGAACCTGCA-
1 ATAAGAAATT-ACCAACTGATCG--GACTGAACCT--AT
**
434723 ATAAGAAATTACCAACTGATCGGTGTTGAACCTAT
1 ATAAGAAATTACCAACTGATCGG-ACTGAACCTAT
* *
434758 ATAAGGAATTACCAGCCTGATCAGGACTGAACCT
1 ATAAGAAATTACCA-ACTGATC-GGACTGAACCT
434792 GTAGAGACTT
Statistics
Matches: 81, Mismatches: 15, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
34 2 0.02
35 27 0.33
36 38 0.47
37 13 0.16
38 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (34 bp):
ATAAGAAATTACCAACTGATCGGACTGAACCTAT
Found at i:436495 original size:13 final size:13
Alignment explanation
Indices: 436477--436501 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
436467 TGACTTTTTG
436477 AGTCAAAGTCAAC
1 AGTCAAAGTCAAC
436490 AGTCAAAGTCAA
1 AGTCAAAGTCAA
436502 TGAGTCAGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.16, T:0.16
Consensus pattern (13 bp):
AGTCAAAGTCAAC
Found at i:436513 original size:19 final size:19
Alignment explanation
Indices: 436491--436549 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
436481 AAAGTCAACA
*
436491 GTCAAAGTCAATGA-GTCAG
1 GTCAAAGTCAA-CATGTCAG
436510 GTCAAAGTCAACATGTCAG
1 GTCAAAGTCAACATGTCAG
* *
436529 GTCAAAGTTAACAGGTCAG
1 GTCAAAGTCAACATGTCAG
436548 GT
1 GT
436550 TGGGTTGACT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 1 0.03
19 35 0.97
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (19 bp):
GTCAAAGTCAACATGTCAG
Found at i:442237 original size:229 final size:234
Alignment explanation
Indices: 441836--442299 Score: 884
Period size: 229 Copynumber: 2.0 Consensus size: 234
441826 TTGGCATTAT
441836 GGTCCACGTTAAAATGTAGAAGCAATTGTTGGTGGAAACAGCCTCTTGAGTTGAGACTCAATGAA
1 GGTCCACGTTAAAATGTAGAAGCAATTGTTGGTGGAAACAGCCTCTTGAGTTGAGACTCAATGAA
441901 CTTGCCAAATTGGAAGAAAGCTTTGTCTTTAACTAGAACCGAGTCAGATCATTTGGTTATACGCA
66 CTTGCCAAATTGGAAGAAAGCTTTGTCTTTAACTAGAACCGAGTCAGATCATTTGGTTATACGCA
441966 ATATATATGGTTTGACCTTTGGCCATAACTTGTTCATACTTC-A-A-ATAT-AACGATATTAATG
131 ATATATATGGTTTGACCTTTGGCCATAACTTGTTCATACTTCAATATATATAAACGATATTAATG
442027 CCAGAATTTCATAATATTGA-TTTGTTAAACACATTTTC
196 CCAGAATTTCATAATATTGATTTTGTTAAACACATTTTC
442065 GGTCCACGTTAAAATGTAGAAGCAATTGTTGGTGGAAACAGCCTCTTGAGTTGAGACTCAATGAA
1 GGTCCACGTTAAAATGTAGAAGCAATTGTTGGTGGAAACAGCCTCTTGAGTTGAGACTCAATGAA
442130 CTTGCCAAATTGGAAGAAAGCTTTGTCTTTAACTAGAACCGAGTCAGATCATTTGGTTATACGCA
66 CTTGCCAAATTGGAAGAAAGCTTTGTCTTTAACTAGAACCGAGTCAGATCATTTGGTTATACGCA
442195 ATATATATGGTTTGACCTTTGGCCATAACTTGTTCATACTTCAAATATATATAAACGATATTAAT
131 ATATATATGGTTTGACCTTTGGCCATAACTTGTTCATACTTC-AATATATATAAACGATATTAAT
442260 GCCAGAATTTCATAATATTGATTTTGTTAAACACATTTTC
195 GCCAGAATTTCATAATATTGATTTTGTTAAACACATTTTC
442300 TAACATGACA
Statistics
Matches: 229, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
229 172 0.75
231 1 0.00
232 1 0.00
233 4 0.02
234 33 0.14
235 18 0.08
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Consensus pattern (234 bp):
GGTCCACGTTAAAATGTAGAAGCAATTGTTGGTGGAAACAGCCTCTTGAGTTGAGACTCAATGAA
CTTGCCAAATTGGAAGAAAGCTTTGTCTTTAACTAGAACCGAGTCAGATCATTTGGTTATACGCA
ATATATATGGTTTGACCTTTGGCCATAACTTGTTCATACTTCAATATATATAAACGATATTAATG
CCAGAATTTCATAATATTGATTTTGTTAAACACATTTTC
Found at i:449072 original size:101 final size:101
Alignment explanation
Indices: 448897--449100 Score: 381
Period size: 101 Copynumber: 2.0 Consensus size: 101
448887 AACATAACAG
448897 ATTTCATGACAAACGCGATCAATGTTGATAAATTTACTTGGTGTCGATCCTCTTGTGGCCTGTCA
1 ATTTCATGACAAACGCGATCAATGTTGATAAATTTACTTGGTGTCGATCCTCTTGTGGCCTGTCA
* *
448962 GAGACGTAAGCAACATGATGGTACAATGTAGAAAGA
66 GAGACGTAAGCAACATAATGGTACAAGGTAGAAAGA
*
448998 ATTTCATGACAAAGGCGATCAATGTTGATAAATTTACTTGGTGTCGATCCTCTTGTGGCCTGTCA
1 ATTTCATGACAAACGCGATCAATGTTGATAAATTTACTTGGTGTCGATCCTCTTGTGGCCTGTCA
449063 GAGACGTAAGCAACATAATGGTACAAGGTAGAAAGA
66 GAGACGTAAGCAACATAATGGTACAAGGTAGAAAGA
449099 AT
1 AT
449101 GGTGTGAAGA
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.28
Consensus pattern (101 bp):
ATTTCATGACAAACGCGATCAATGTTGATAAATTTACTTGGTGTCGATCCTCTTGTGGCCTGTCA
GAGACGTAAGCAACATAATGGTACAAGGTAGAAAGA
Found at i:451324 original size:12 final size:13
Alignment explanation
Indices: 451303--451361 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 13
451293 AGACGTAAAC
451303 TTTTTAAAATTTA
1 TTTTTAAAATTTA
451316 TTTTT-AAATTTA
1 TTTTTAAAATTTA
* *
451328 -TTTT-CAATTTT
1 TTTTTAAAATTTA
*
451339 TTTTGTAAAAATTAA
1 TTTT-T-AAAATTTA
451354 TTTTTAAA
1 TTTTTAAA
451362 CGCATTAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
11 9 0.24
12 10 0.27
13 9 0.24
14 1 0.03
15 8 0.22
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (13 bp):
TTTTTAAAATTTA
Found at i:451658 original size:18 final size:19
Alignment explanation
Indices: 451623--451659 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
451613 CACGGAATGT
451623 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
451643 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
451660 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:451864 original size:30 final size:32
Alignment explanation
Indices: 451808--451872 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
451798 AAATTGTAAA
* *
451808 ATATTTATATATTTTCTTTAAAAAATTAATAT
1 ATATTTATATAATTTCTTTAAAAAATTAAAAT
*
451840 ATATTTATATAATTT-TTT-ACAAATTAAAAT
1 ATATTTATATAATTTCTTTAAAAAATTAAAAT
451870 ATA
1 ATA
451873 AAAAAGGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 13 0.43
31 3 0.10
32 14 0.47
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (32 bp):
ATATTTATATAATTTCTTTAAAAAATTAAAAT
Found at i:452713 original size:15 final size:15
Alignment explanation
Indices: 452676--452721 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
452666 TACTCATTAC
452676 ATTTAGGG-TTAGAG
1 ATTTAGGGTTTAGAG
452690 ATTTAAGGGTTTAG-G
1 ATTT-AGGGTTTAGAG
452705 TATTTAGGGATTTAGAG
1 -ATTTAGGG-TTTAGAG
452722 TAATGGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.15
15 9 0.33
16 13 0.48
17 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.39
Consensus pattern (15 bp):
ATTTAGGGTTTAGAG
Found at i:454691 original size:194 final size:195
Alignment explanation
Indices: 454362--454750 Score: 640
Period size: 194 Copynumber: 2.0 Consensus size: 195
454352 ACGATTTCTT
* * * *
454362 TAAGAATATCATCAGCATATCGGAATCGACCCTGAAATAATCTTCGATTCCATTCCTGCCACAAG
1 TAAGAATATCATCAGCAGATCAGAATCGACCCTGAAATAATCTCCGATTCCATTCCTACCACAAG
*
454427 AAATAGATGAGAGCATTCCACGAAATCTTCAAAATGGTGGTCAAGAGTGATTTTCCTTTTCAAGA
66 AAATAGATGAGAGCATTCCACGAAATCTTCAAAATGATGGTCAAGAGTGATTTTCCTTTTCAAGA
454492 AGCACAAGCACGAAATACCATTACATCCCCAAGAC-AAACAT-A-AATATCATCTCATTCATGCT
131 AGCACAAGCACGAAATACCATTACAT-CCCAAGACAAAACATAATAAT-TCATCTCATTCATGCT
454554 AA
194 AA
* *
454556 TAAGAATATCATCAGCAGATCAGAATCGGCCCTGAAATAATCTCCGATTTCATTCCTACCACAAG
1 TAAGAATATCATCAGCAGATCAGAATCGACCCTGAAATAATCTCCGATTCCATTCCTACCACAAG
* *
454621 AAATAGATGAGAGCATTCCACGAAATCTTTAAAATGATGGTTAAGAGTGATTTTCCTTTTCAAGA
66 AAATAGATGAGAGCATTCCACGAAATCTTCAAAATGATGGTCAAGAGTGATTTTCCTTTTCAAGA
* *
454686 AGCACAAGCATGAGATACCATTACATCCCAAGACAAAACATAATAATTCATCTCATTCATGCTAA
131 AGCACAAGCACGAAATACCATTACATCCCAAGACAAAACATAATAATTCATCTCATTCATGCTAA
454751 GGGTAGATCT
Statistics
Matches: 181, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
193 8 0.04
194 151 0.83
195 19 0.10
196 3 0.02
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (195 bp):
TAAGAATATCATCAGCAGATCAGAATCGACCCTGAAATAATCTCCGATTCCATTCCTACCACAAG
AAATAGATGAGAGCATTCCACGAAATCTTCAAAATGATGGTCAAGAGTGATTTTCCTTTTCAAGA
AGCACAAGCACGAAATACCATTACATCCCAAGACAAAACATAATAATTCATCTCATTCATGCTAA
Found at i:456753 original size:3 final size:3
Alignment explanation
Indices: 456745--456849 Score: 165
Period size: 3 Copynumber: 35.0 Consensus size: 3
456735 TTTAATATTT
*
456745 ATA ATA ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
456793 ATG ATA ATA ATA ATA ATA ATA ATA ATA ATT ATA ATT ATA ATA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
456841 ATA ATA ATA
1 ATA ATA ATA
456850 TTTATAATAT
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 92 1.00
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:457352 original size:112 final size:113
Alignment explanation
Indices: 457078--457736 Score: 987
Period size: 114 Copynumber: 5.9 Consensus size: 113
457068 GATAGAGTTA
* *
457078 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
* * * * * * * * * *
457143 GAACTCTAC-CTGGCAATGTTGATCCATCAAATGATTAATTCAAGCAAAAGA
63 GAACT-TTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGG
*
457194 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
457259 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT-AAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAA-TTGATGAATTCAGGTAAAAGG
457307 TTGAAC-AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
457371 CTTTCTCTGGAAAAGCTAATCCATCAATTGATGAATTCAGGTAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGG
457419 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTC-TTCCTTCTTCAGATGAGTTCTTCTCATTATGA
*
457484 ACTTTCTCTGGAAAAGCTAATCCATCAATTTGATGAATTCAGGTAAAAGG
65 ACTTTCTCTGGAAAAGATAATCCATCAA-TTGATGAATTCAGGTAAAAGG
457534 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG-A
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
457598 CTTTCTCT-G--AA-ATGATCCATCAAATGATGGATTCAGGTAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGG
*
457642 TTGAACAAATTCTTCTCA-T-TGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
457705 CTTTCTCTGGAAATGATGATCCATCAAATGAT
66 CTTTCTCTGGAAAAGATAATCCATCAATTGAT
457737 AGATTTGAAT
Statistics
Matches: 513, Mismatches: 19, Indels: 27
0.92 0.03 0.05
Matches are distributed among these distances:
106 41 0.08
107 10 0.02
108 38 0.07
109 10 0.02
110 3 0.01
111 32 0.06
112 97 0.19
113 82 0.16
114 102 0.20
115 53 0.10
116 45 0.09
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (113 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGG
Found at i:458331 original size:83 final size:83
Alignment explanation
Indices: 458192--458801 Score: 1106
Period size: 83 Copynumber: 7.4 Consensus size: 83
458182 GTTCTTACCA
*
458192 AAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACACATTCATCTTCTAAA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCTAAA
458256 TTCAATGATTTGTTCTGCC
65 TTCAATGATTTGTTCTGCC
*
458275 AAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAAT
458340 TCAATGATTTGTTCTGCC
66 TCAATGATTTGTTCTGCC
*
458358 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTTATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAAT
*
458423 TCAATGATATGTTCTGCC
66 TCAATGATTTGTTCTGCC
*
458441 AAACCAGATCAAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCTAAA
1 AAACCAGATC-AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAA
458506 TTCAATGATTTG-TCTGCC
65 TTCAATGATTTGTTCTGCC
458524 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-ACACATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAAT
*
458588 TCAAT-AATT-TTCTGCC
66 TCAATGATTTGTTCTGCC
458604 AAACCA-ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAAT
458668 TCAATGATTTGTTCTGCC
66 TCAATGATTTGTTCTGCC
458686 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAAT
458751 TCAATGATTTGTTCTGCC
66 TCAATGATTTGTTCTGCC
458769 AAACCAGATCAGATAACTCAAAGAACACTTCCA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCA
458802 AGATAACTCA
Statistics
Matches: 509, Mismatches: 11, Indels: 14
0.95 0.02 0.03
Matches are distributed among these distances:
79 38 0.07
80 39 0.08
81 27 0.05
82 49 0.10
83 293 0.58
84 63 0.12
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (83 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAAT
TCAATGATTTGTTCTGCC
Found at i:458809 original size:23 final size:23
Alignment explanation
Indices: 458779--458824 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
458769 AAACCAGATC
458779 AGATAACTCAAAGAACACTTCCA
1 AGATAACTCAAAGAACACTTCCA
458802 AGATAACTCAAAGAACACTTCCA
1 AGATAACTCAAAGAACACTTCCA
458825 GAAGATGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.26, G:0.09, T:0.17
Consensus pattern (23 bp):
AGATAACTCAAAGAACACTTCCA
Found at i:458887 original size:105 final size:106
Alignment explanation
Indices: 458696--458906 Score: 415
Period size: 105 Copynumber: 2.0 Consensus size: 106
458686 AAACCAGATC
458696 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAATTCAATGATTT
1 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAATTCAATGATTT
458761 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
66 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
458802 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATT-ATCTTCTAAATTCAATGATTT
1 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAATTCAATGATTT
458866 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
66 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
458907 GAAGATGCTA
Statistics
Matches: 105, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
105 62 0.59
106 43 0.41
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (106 bp):
AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAATTCAATGATTT
GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
Found at i:458931 original size:188 final size:185
Alignment explanation
Indices: 458613--458985 Score: 703
Period size: 188 Copynumber: 2.0 Consensus size: 185
458603 CAAACCAATC
458613 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAATTCAATGATTT
1 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAATTCAATGATTT
458678 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATC
66 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATC
458743 TTCTAAATTCAATGATTTGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
131 TTCTAAA--CAATGATTTGTTCTGCCAAA-CAGATCAGA-AACTCAAAGAACACTTCCA
458802 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATT-ATCTTCTAAATTCAATGATTT
1 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAATTCAATGATTT
458866 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATC
66 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATC
458931 TTCTAAACAATGATTTGTTCTGCCAAACAGATCAGAAACTCAAAGAACACTTCCA
131 TTCTAAACAATGATTTGTTCTGCCAAACAGATCAGAAACTCAAAGAACACTTCCA
458986 GAAGATGCTA
Statistics
Matches: 184, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
184 19 0.10
185 9 0.05
186 20 0.11
188 93 0.51
189 43 0.23
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (185 bp):
AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAATTCAATGATTT
GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATC
TTCTAAACAATGATTTGTTCTGCCAAACAGATCAGAAACTCAAAGAACACTTCCA
Found at i:459071 original size:161 final size:164
Alignment explanation
Indices: 458802--459191 Score: 698
Period size: 161 Copynumber: 2.4 Consensus size: 164
458792 AACACTTCCA
*
458802 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTATCTTCTAAATTCAATGATTTG
1 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATCATCTTCTAAATTCAATGATTTG
*
458867 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCT
66 TTCTGCCAAACCAGATAAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCT
458932 TCTAAA-CAATGATTTGTTCTGCCAAA-CAGATC
131 TCTAAATCAATGATTTGTTCTGCCAAACCAGATC
458964 AGA-AACTCAAAGAACACTTCCAGAAGATGCTATGAAC-CTATCATCTTCTAAATTCAATGATTT
1 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAC-ATCATCTTCTAAATTCAATGATTT
459027 GTTCTGCCAAACCAGATAAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATC
65 GTTCTGCCAAACCAGATAAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATC
459092 TTCTAAATTCAATGATTTGTTCTGCCAAACCAGATC
130 TTCTAAA-TCAATGATTTGTTCTGCCAAACCAGATC
*
459128 AGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACACATTCATCTTCTAAATTCAATGATT
1 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACA-TCATCTTCTAAATTCAATGATT
459192 GGACTAGGAT
Statistics
Matches: 218, Mismatches: 3, Indels: 10
0.94 0.01 0.04
Matches are distributed among these distances:
160 1 0.00
161 128 0.59
162 3 0.01
163 20 0.09
164 9 0.04
165 34 0.16
166 23 0.11
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (164 bp):
AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATCATCTTCTAAATTCAATGATTTG
TTCTGCCAAACCAGATAAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCT
TCTAAATCAATGATTTGTTCTGCCAAACCAGATC
Found at i:459120 original size:83 final size:83
Alignment explanation
Indices: 458802--459191 Score: 704
Period size: 83 Copynumber: 4.8 Consensus size: 83
458792 AACACTTCCA
458802 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATT-ATCTTCTAAATTCAATGATTT
1 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAATTCAATGATTT
458866 GTTCTGCCAAACCAGATC
66 GTTCTGCCAAACCAGATC
458884 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAA--CAATGATTT
1 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAATTCAATGATTT
458947 GTTCTGCCAAA-CAGATC
66 GTTCTGCCAAACCAGATC
458964 AGA-AACTCAAAGAACACTTCCAGAAGATGCTATGAAC-C-TATCATCTTCTAAATTCAATGATT
1 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACAT-TCATCTTCTAAATTCAATGATT
*
459026 TGTTCTGCCAAACCAGATA
65 TGTTCTGCCAAACCAGATC
459045 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAATTCAATGATTT
1 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAATTCAATGATTT
459110 GTTCTGCCAAACCAGATC
66 GTTCTGCCAAACCAGATC
*
459128 AGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACACATTCATCTTCTAAATTCAATGATT
1 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAATTCAATGATT
459192 GGACTAGGAT
Statistics
Matches: 297, Mismatches: 3, Indels: 15
0.94 0.01 0.05
Matches are distributed among these distances:
77 1 0.00
78 13 0.04
79 34 0.11
80 29 0.10
81 28 0.09
82 77 0.26
83 114 0.38
84 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (83 bp):
AGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAATTCAATGATTT
GTTCTGCCAAACCAGATC
Found at i:460331 original size:16 final size:16
Alignment explanation
Indices: 460310--460396 Score: 84
Period size: 17 Copynumber: 5.1 Consensus size: 16
460300 ATCCCCCCTC
460310 TTTTCTTTTTTTTTCT
1 TTTTCTTTTTTTTTCT
*
460326 TTTTCTTTTTCTCTCTTTT
1 TTTTCTTTTT-T-T-TTCT
* *
460345 TTTTATTTTTCTTTTAT
1 TTTTCTTTTT-TTTTCT
460362 TTTTCTTTCTTTTTTCT
1 TTTTCTTT-TTTTTTCT
*
460379 TTCTTCTCTTTTTTTCT
1 TT-TTCTTTTTTTTTCT
460396 T
1 T
460397 CAAGCATAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
16 10 0.17
17 27 0.45
18 9 0.15
19 14 0.23
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCTTTTTTTTTCT
Found at i:460342 original size:26 final size:26
Alignment explanation
Indices: 460313--460390 Score: 86
Period size: 25 Copynumber: 2.9 Consensus size: 26
460303 CCCCCTCTTT
460313 TCTTTTTTTTTCTTTTTCTTTTTCTC
1 TCTTTTTTTTTCTTTTTCTTTTTCTC
* * *
460339 TC-TTTTTTTTATTTTTCTTTTATTTT
1 TCTTTTTTTTTCTTTTTCTTTT-TCTC
460365 TCTTTCTTTTTTCTTTCTTCTCTTTT
1 TCTTT-TTTTTTCTTT-TTCT-TTTT
460391 TTTCTTCAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
25 18 0.42
26 6 0.14
27 2 0.05
28 9 0.21
29 5 0.12
30 3 0.07
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (26 bp):
TCTTTTTTTTTCTTTTTCTTTTTCTC
Found at i:460355 original size:41 final size:46
Alignment explanation
Indices: 460310--460393 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
460300 ATCCCCCCTC
460310 TTTTCTTTT-TTTTTC-TT-TTTCTT-TTTC-TCTCTTTTTTTTAT
1 TTTTCTTTTATTTTTCTTTCTTTCTTCTTTCTTCTCTTTTTTTTAT
*
460351 TTTTCTTTTATTTTTCTTTCTTTTTTCTTTCTTCTCTTTTTTT
1 TTTTCTTTTATTTTTCTTTCTTTCTTCTTTCTTCTCTTTTTTT
460394 CTTCAAGCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
41 9 0.24
42 6 0.16
43 2 0.05
44 5 0.14
45 4 0.11
46 11 0.30
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.82
Consensus pattern (46 bp):
TTTTCTTTTATTTTTCTTTCTTTCTTCTTTCTTCTCTTTTTTTTAT
Found at i:460367 original size:30 final size:30
Alignment explanation
Indices: 460307--460391 Score: 100
Period size: 30 Copynumber: 2.7 Consensus size: 30
460297 TTGATCCCCC
*
460307 CTCTTTTCTTTTTTTTTCTTTTTCTTTTTCT
1 CTCTTTT-TTTTTTTTTCTTTTTATTTTTCT
460338 CTCTTTTTTTTATTTTTC-TTTTATTTTTCT
1 CTCTTTTTTTT-TTTTTCTTTTTATTTTTCT
* *
460368 TTCTTTTTTCTTTCTTCTCTTTTT
1 CTCTTTTTT-TTT-TTTTCTTTTT
460392 TTCTTCAAGC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
30 24 0.51
31 19 0.40
32 4 0.09
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (30 bp):
CTCTTTTTTTTTTTTTCTTTTTATTTTTCT
Found at i:460381 original size:11 final size:10
Alignment explanation
Indices: 460310--460393 Score: 73
Period size: 11 Copynumber: 8.2 Consensus size: 10
460300 ATCCCCCCTC
460310 TTTTCTTTTT
1 TTTTCTTTTT
460320 TTTTCTTTTTCT
1 TTTTC-TTTT-T
* *
460332 TTTTCTCTCT
1 TTTTCTTTTT
*
460342 TTTT-TTTAT
1 TTTTCTTTTT
460351 TTTTCTTTTAT
1 TTTTCTTTT-T
460362 TTTTCTTTCTT
1 TTTTCTTT-TT
*
460373 TTTTC-TTTC
1 TTTTCTTTTT
*
460382 TTCTCTTTTT
1 TTTTCTTTTT
460392 TT
1 TT
460394 CTTCAAGCAT
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
9 12 0.20
10 20 0.33
11 21 0.35
12 7 0.12
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:470857 original size:15 final size:13
Alignment explanation
Indices: 470825--470862 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
470815 TCTGACAGAA
470825 AAAT-AAATAATG
1 AAATAAAATAATG
470837 AAATAAAATAATTG
1 AAATAAAATAA-TG
470851 CAAATAAAATAA
1 -AAATAAAATAA
470863 ATAAAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 6 0.26
14 2 0.09
15 11 0.48
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (13 bp):
AAATAAAATAATG
Found at i:470878 original size:32 final size:30
Alignment explanation
Indices: 470824--470903 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 30
470814 CTCTGACAGA
*
470824 AAAATAAATAATGAAATAAAATA-ATTGCAAAT
1 AAAATAAATAA--AAATAAAATATA-TGAAAAT
470856 AAAATAAATAAAACATATAAATATATGAAAAT
1 AAAATAAATAAAA-ATA-AAATATATGAAAAT
470888 AATAAGTAAATAAAAA
1 AA-AA-TAAATAAAAA
470904 ATTTTGAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
30 2 0.05
31 3 0.07
32 24 0.57
33 4 0.10
34 9 0.21
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.24
Consensus pattern (30 bp):
AAAATAAATAAAAATAAAATATATGAAAAT
Found at i:471575 original size:98 final size:97
Alignment explanation
Indices: 471400--471585 Score: 227
Period size: 98 Copynumber: 1.9 Consensus size: 97
471390 ATATTATTTA
* *
471400 TTTAAAATATCAGAAAAGAACTTCTAGGTGCTTTAAGACAGCTCTTTTCTTTGATATTGATAAAT
1 TTTAAAATATCAGAAAAGAACATCCAGGTGCTTTAAGACAGCTCTTTTCTTTGATATTGATAAAT
* *
471465 ATTAATTTAAATAATATTGTTTAATTTTTAATT
66 ATAAATTTAAATAAT-TTATTTAATTTTTAATT
* * * *
471498 TTTAAAATATCAGAATAGGACATCCAGTTG-TATTAAGACTG-TCATTTTCTTTGATATTGA-AA
1 TTTAAAATATCAGAAAAGAACATCCAGGTGCT-TTAAGACAGCTC-TTTTCTTTGATATTGATAA
471560 A-ATAAATATTAAAATAATTTATTTAA
64 ATATAAAT-TT-AAATAATTTATTTAA
471586 AATAAATATT
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
96 5 0.07
97 15 0.20
98 56 0.74
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.42
Consensus pattern (97 bp):
TTTAAAATATCAGAAAAGAACATCCAGGTGCTTTAAGACAGCTCTTTTCTTTGATATTGATAAAT
ATAAATTTAAATAATTTATTTAATTTTTAATT
Done.