Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007711.1 Hibiscus syriacus cultivar Beakdansim tig00109926_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: 1768490
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 7 of 8
Found at i:1487073 original size:38 final size:38
Alignment explanation
Indices: 1486686--1487072 Score: 482
Period size: 38 Copynumber: 10.1 Consensus size: 38
1486676 ATAAATAAAG
* * *
1486686 AAAAA-TATTTTTTAAAACTATATAATATATATGTTTTT
1 AAAAACTAATTTTCAAAACTATATAATATATAT-ATTTT
* * *
1486724 AAAGAAAATAATTTTCAAAACCATATAATATATAGT-TTTGAA
1 -AA-AAACTAATTTTCAAAACTATATAATATATA-TATTT--T
* * *
1486766 AAAAAATAATTTTCAAAATTATGTAATATATA-ATTTTT
1 AAAAACTAATTTTCAAAACTATATAATATATATA-TTTT
1486804 AAAAACTAATTTTCAAAACTATATAATATATATATTTT
1 AAAAACTAATTTTCAAAACTATATAATATATATATTTT
*
1486842 AAAAACTAATTTTCAAAATTATATAATATATATATTTT
1 AAAAACTAATTTTCAAAACTATATAATATATATATTTT
1486880 AAAAACTAATTTTCAAAACTATATAATATATAT-TTTT
1 AAAAACTAATTTTCAAAACTATATAATATATATATTTT
*
1486917 TAAAACTAATTTTCAAAAC--TATAATATATAT-TTTT
1 AAAAACTAATTTTCAAAACTATATAATATATATATTTT
1486952 AAAAACTAATTTTCAAAACTATATAATATATATATTTT
1 AAAAACTAATTTTCAAAACTATATAATATATATATTTT
* *
1486990 AAAAAACTATTTTTCAAAACTATATAATATATATATTTC
1 -AAAAACTAATTTTCAAAACTATATAATATATATATTTT
* ** * *
1487029 AAAAAATTGTTTTAAAAACTATATAATATATATGGTTTT
1 AAAAACTAATTTTCAAAACTATATAATATATAT-ATTTT
1487068 AAAAA
1 AAAAA
1487073 TGTTTTTTTA
Statistics
Matches: 312, Mismatches: 23, Indels: 26
0.86 0.06 0.07
Matches are distributed among these distances:
35 34 0.11
37 34 0.11
38 135 0.43
39 47 0.15
40 36 0.12
41 25 0.08
42 1 0.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (38 bp):
AAAAACTAATTTTCAAAACTATATAATATATATATTTT
Found at i:1487094 original size:149 final size:148
Alignment explanation
Indices: 1486686--1487073 Score: 494
Period size: 149 Copynumber: 2.6 Consensus size: 148
1486676 ATAAATAAAG
* * * * * *
1486686 AAAAA-TATTTTTTAAAACTATATAATATATATGTTTTTAAAGAAAATAATTTTCAAAACCATAT
1 AAAAACTAATTTTCAAAACTATATAATATATA--TATTTCAA-AAAATAATTTTAAAAACTATAT
*
1486750 AATATATA-GTTTTGAAAAAAAATAATTTTCAAAATTATGTAATATATAATTTTTAAAAACTAAT
63 AATATATATGTTTT----AAAAATAATTTTCAAAA-CA--TAATATATAATTTTTAAAAACTAAT
1486814 TTTCAAAACTATATAATATATATATTTT
121 TTTCAAAACTATATAATATATATATTTT
* * * *
1486842 AAAAACTAATTTTCAAAATTATATAATATATATATTTTAAAAACTAATTTTCAAAACTATATAAT
1 AAAAACTAATTTTCAAAACTATATAATATATATATTTCAAAAAATAATTTTAAAAACTATATAAT
* *
1486907 ATATATTTTTTAAAACTAATTTTCAAAACTATAATATAT-ATTTTTAAAAACTAATTTTCAAAAC
66 ATATATGTTTTAAAAATAATTTTCAAAAC-ATAATATATAATTTTTAAAAACTAATTTTCAAAAC
1486971 TATATAATATATATATTTT
130 TATATAATATATATATTTT
* **
1486990 AAAAAACTATTTTTCAAAACTATATAATATATATATTTCAAAAAATTGTTTTAAAAACTATATAA
1 -AAAAACTAATTTTCAAAACTATATAATATATATATTTCAAAAAATAATTTTAAAAACTATATAA
1487055 TATATATGGTTTTAAAAAT
65 TATATAT-GTTTTAAAAAT
1487074 GTTTTTTTAA
Statistics
Matches: 208, Mismatches: 19, Indels: 16
0.86 0.08 0.07
Matches are distributed among these distances:
148 44 0.21
149 72 0.35
150 9 0.04
151 17 0.08
154 28 0.13
155 10 0.05
156 5 0.02
157 23 0.11
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (148 bp):
AAAAACTAATTTTCAAAACTATATAATATATATATTTCAAAAAATAATTTTAAAAACTATATAAT
ATATATGTTTTAAAAATAATTTTCAAAACATAATATATAATTTTTAAAAACTAATTTTCAAAACT
ATATAATATATATATTTT
Found at i:1487134 original size:2 final size:2
Alignment explanation
Indices: 1487127--1487164 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1487117 GTTTGCAAAC
1487127 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
1487165 CGTATAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1488081 original size:10 final size:10
Alignment explanation
Indices: 1488068--1488124 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
1488058 ACACGCTGGG
*
1488068 CATCCTAGGC
1 CATCCGAGGC
1488078 CATCCGAGAG-
1 CATCCGAG-GC
1488088 CATCCGAGGC
1 CATCCGAGGC
*
1488098 CATCCCAGAG-
1 CATCCGAG-GC
1488108 CATCCGAGGC
1 CATCCGAGGC
1488118 CATCCGA
1 CATCCGA
1488125 ACGAGCTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 2 0.05
10 36 0.90
11 2 0.05
ACGTcount: A:0.25, C:0.39, G:0.25, T:0.12
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:1488092 original size:20 final size:20
Alignment explanation
Indices: 1488067--1488124 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1488057 AACACGCTGG
*
1488067 GCATCCTAGGCCATCCGAGA
1 GCATCCGAGGCCATCCGAGA
*
1488087 GCATCCGAGGCCATCCCAGA
1 GCATCCGAGGCCATCCGAGA
1488107 GCATCCGAGGCCATCCGA
1 GCATCCGAGGCCATCCGA
1488125 ACGAGCTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.24, C:0.38, G:0.26, T:0.12
Consensus pattern (20 bp):
GCATCCGAGGCCATCCGAGA
Found at i:1488170 original size:23 final size:23
Alignment explanation
Indices: 1488112--1488175 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
1488102 CCAGAGCATC
* * *
1488112 CGAGGCCATCCGAACGAGCTATA
1 CGAGGGCAACCGAGCGAGCTATA
*
1488135 CGAGGGCAACCGAGCGAGCTATG
1 CGAGGGCAACCGAGCGAGCTATA
1488158 CGAGGG-AAGCCGAGCGAG
1 CGAGGGCAA-CCGAGCGAG
1488176 GGTAGGTCGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 2 0.06
23 34 0.94
ACGTcount: A:0.28, C:0.27, G:0.38, T:0.08
Consensus pattern (23 bp):
CGAGGGCAACCGAGCGAGCTATA
Found at i:1488212 original size:29 final size:28
Alignment explanation
Indices: 1488179--1488263 Score: 125
Period size: 29 Copynumber: 2.9 Consensus size: 28
1488169 GAGCGAGGGT
1488179 AGGTCGCCCGAAGTGCATGGCGACCTACA
1 AGGTCGCCCGAAG-GCATGGCGACCTACA
*
1488208 AGGTCGCCCGGAGGGCATGGCGACCTACA
1 AGGTCGCCC-GAAGGCATGGCGACCTACA
*
1488237 AGGTCGCCCGGAAGGCATGTCGACCTA
1 AGGTCGCCC-GAAGGCATGGCGACCTA
1488264 TGTGTTGGGA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
29 49 0.94
30 3 0.06
ACGTcount: A:0.22, C:0.31, G:0.34, T:0.13
Consensus pattern (28 bp):
AGGTCGCCCGAAGGCATGGCGACCTACA
Found at i:1488309 original size:12 final size:12
Alignment explanation
Indices: 1488292--1488316 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1488282 TGCCATGCAA
1488292 CACGTTCATTCT
1 CACGTTCATTCT
1488304 CACGTTCATTCT
1 CACGTTCATTCT
1488316 C
1 C
1488317 TCTGTTTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (12 bp):
CACGTTCATTCT
Found at i:1494262 original size:22 final size:21
Alignment explanation
Indices: 1494227--1494269 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1494217 CTTATTCTTA
*
1494227 TTTTATTTATTCAATTATATT
1 TTTTATTTAATCAATTATATT
1494248 TTTTATTTTAATCAATTATATT
1 TTTTA-TTTAATCAATTATATT
1494270 AATTTAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTATTTAATCAATTATATT
Found at i:1494711 original size:41 final size:40
Alignment explanation
Indices: 1494624--1494725 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 40
1494614 GTATAAAATA
1494624 TTAAATATGTGATGAATAAAATATTAAATAAGAATATATTTAT
1 TTAAATATGTGATGAAT---ATATTAAATAAGAATATATTTAT
*
1494667 TTAAATATGTGATGAATATA-TAATTGAGAGAATATATTTAT
1 TTAAATATGTGATGAATATATTAAAT-A-AGAATATATTTAT
*
1494708 TTAAATATGTGATCAATA
1 TTAAATATGTGATGAATA
1494726 AAATATTAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
39 4 0.07
40 4 0.07
41 30 0.55
43 17 0.31
ACGTcount: A:0.47, C:0.01, G:0.12, T:0.40
Consensus pattern (40 bp):
TTAAATATGTGATGAATATATTAAATAAGAATATATTTAT
Found at i:1495876 original size:186 final size:184
Alignment explanation
Indices: 1495515--1495894 Score: 609
Period size: 187 Copynumber: 2.0 Consensus size: 184
1495505 TATATAAAAA
* *
1495515 TTAAATATTTTTTAATTAAAAAAATAGTTTATATTTAATTTAAATAATATATAATTATAAAATAA
1 TTAAA-ATTTTTTAATTAAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAATAA
* * *
1495580 AAATTTATATAAATTTTTTAATTAATTAATATTGATTTATGTTTAAAAGTTATTGGATCTTAAAT
65 AAATTTATATAAATTTTTTAATTAATTAATATTGATTTATATTTAAAACTTATTGGATATTAAAT
* *
1495645 TATTAATTGAATTTTAAATGGTTTGGGCTGAGCTCATACGTTATATATAATATAT
130 TATTAATTGAATTTTAAATGATTTGGGCTGAACTCATACGTTATATATAATATAT
1495700 TTAAAATTTTTTAATTCAAAAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAAT
1 TTAAAATTTTTTAATT---AAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAAT
1495765 AAAAATTTATATAAATTTTTTAATTAATTAATATTGATTTATATTT-AAACTTATTGGATATTAA
63 AAAAATTTATATAAATTTTTTAATTAATTAATATTGATTTATATTTAAAACTTATTGGATATTAA
** * * *
1495829 ATTATTAATTGTGTTTTAAATTATTTGGGCTTAACTCATATGTTATATATAATATAT
128 ATTATTAATTGAATTTTAAATGATTTGGGCTGAACTCATACGTTATATATAATATAT
1495886 TTAAAATTT
1 TTAAAATTT
1495895 AATTTCGGTT
Statistics
Matches: 180, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
184 11 0.06
185 5 0.03
186 75 0.42
187 89 0.49
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (184 bp):
TTAAAATTTTTTAATTAAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAA
AATTTATATAAATTTTTTAATTAATTAATATTGATTTATATTTAAAACTTATTGGATATTAAATT
ATTAATTGAATTTTAAATGATTTGGGCTGAACTCATACGTTATATATAATATAT
Found at i:1497599 original size:15 final size:15
Alignment explanation
Indices: 1497559--1497626 Score: 77
Period size: 15 Copynumber: 4.7 Consensus size: 15
1497549 TTATATAAAT
*
1497559 ATTATTTTTTATTAA
1 ATTATTTTTTATTTA
* * * *
1497574 AATAATATTTATATA
1 ATTATTTTTTATTTA
1497589 ATTATTTTTTATTTA
1 ATTATTTTTTATTTA
1497604 A--ATTTTTTATTTA
1 ATTATTTTTTATTTA
1497617 ATTATTTTTT
1 ATTATTTTTT
1497627 GTGCTAATTA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
13 13 0.31
15 29 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTATTTTTTATTTA
Found at i:1497613 original size:28 final size:29
Alignment explanation
Indices: 1497559--1497626 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 29
1497549 TTATATAAAT
1497559 ATTATTTTTTATTAAAATAATATTTATATA
1 ATTATTTTTTATTAAAAT-ATATTTATATA
* * *
1497589 ATTATTTTTTATTTAAAT-TTTTTATTTA
1 ATTATTTTTTATTAAAATATATTTATATA
1497617 ATTATTTTTT
1 ATTATTTTTT
1497627 GTGCTAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 18 0.51
30 17 0.49
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (29 bp):
ATTATTTTTTATTAAAATATATTTATATA
Found at i:1497619 original size:12 final size:13
Alignment explanation
Indices: 1497592--1497617 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1497582 TTATATAATT
1497592 ATTTTTTATTTAA
1 ATTTTTTATTTAA
1497605 ATTTTTTATTTAA
1 ATTTTTTATTTAA
1497618 TTATTTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTTTATTTAA
Found at i:1499361 original size:42 final size:42
Alignment explanation
Indices: 1499271--1499361 Score: 94
Period size: 42 Copynumber: 2.2 Consensus size: 42
1499261 ATAATGATAC
* * *
1499271 CCAA-CCCTCCAGTTCAGATGCAATCTCCTCAGGGGTATATG
1 CCAAGCCCACCAGTTCAGATGCAATCTCCACAGGGGTACATG
* * * * *
1499312 CCAAGCCCACCAGTTTATATGCCATCTCCACAGGGTTACATT
1 CCAAGCCCACCAGTTCAGATGCAATCTCCACAGGGGTACATG
*
1499354 CCTAGCCC
1 CCAAGCCC
1499362 TCAGGGTTAC
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 4 0.10
42 36 0.90
ACGTcount: A:0.24, C:0.35, G:0.16, T:0.24
Consensus pattern (42 bp):
CCAAGCCCACCAGTTCAGATGCAATCTCCACAGGGGTACATG
Found at i:1499368 original size:21 final size:21
Alignment explanation
Indices: 1499342--1499411 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
1499332 GCCATCTCCA
* *
1499342 CAGGGTTACATTCCTAGCCCT
1 CAGGGTTACATTCCTATCCCC
1499363 CAGGGTTACATTCCTATCCCAC
1 CAGGGTTACATTCCTATCCC-C
* *
1499385 CA-GGTTACATGCCTATCCCG
1 CAGGGTTACATTCCTATCCCC
1499405 CAGGGTT
1 CAGGGTT
1499412 TTATGACACC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.05
21 39 0.91
22 2 0.05
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.27
Consensus pattern (21 bp):
CAGGGTTACATTCCTATCCCC
Found at i:1499966 original size:34 final size:34
Alignment explanation
Indices: 1499918--1499990 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
1499908 TTAAATGTTT
*
1499918 TTAATATACAAATTATAGTATTCGAAATATAAAA
1 TTAAAATACAAATTATAGTATTCGAAATATAAAA
* * *
1499952 TTAAAATACAAATTATGGTATTCGAAATTTAACA
1 TTAAAATACAAATTATAGTATTCGAAATATAAAA
1499986 TTAAA
1 TTAAA
1499991 TTCAACTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCGAAATATAAAA
Found at i:1500209 original size:24 final size:23
Alignment explanation
Indices: 1500182--1500232 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1500172 TCAATGTCAG
* * *
1500182 CCAACTTATCACTTCACATTTTTT
1 CCAACTTATC-CATAACATTTTAT
*
1500206 CCAATTTATCCATAACATTTTAT
1 CCAACTTATCCATAACATTTTAT
1500229 CCAA
1 CCAA
1500233 TATATTCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.41
Consensus pattern (23 bp):
CCAACTTATCCATAACATTTTAT
Found at i:1500287 original size:63 final size:64
Alignment explanation
Indices: 1500182--1500306 Score: 198
Period size: 63 Copynumber: 2.0 Consensus size: 64
1500172 TCAATGTCAG
* *
1500182 CCAACTTATCACTTCACATTTTTTCCAATTTATCCATAACATTTTATCCAATATATTCAAACAA
1 CCAACTGATCACTTCACATTTATTCCAATTTATCCATAACATTTTATCCAATATATTCAAACAA
* * *
1500246 CCAACTGATGACTTCACATTTATT-CAATTTATTCATAACATTTTATCCAATTTATTCAAAC
1 CCAACTGATCACTTCACATTTATTCCAATTTATCCATAACATTTTATCCAATATATTCAAAC
1500307 TTCACATAAC
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
63 35 0.62
64 21 0.38
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (64 bp):
CCAACTGATCACTTCACATTTATTCCAATTTATCCATAACATTTTATCCAATATATTCAAACAA
Found at i:1500629 original size:140 final size:138
Alignment explanation
Indices: 1500348--1500712 Score: 543
Period size: 140 Copynumber: 2.6 Consensus size: 138
1500338 ATCAAATTTC
* * *
1500348 ACATGAGTAACATAATAGGGTAATGATAATATATTCTCTGACAAAATAATGGAAGGCGCGCCCCC
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCC
* * * * *
1500413 GGGAACGCACTTTTACCACTTTGCCAAGTCTCCTAAGAAATAATAGGTACTAACATAAATAGTTA
66 AGGAACGCGCTTTCACCACTTTACCAAGTCTCCTAAAAAATAATAGGTACTAACATAAATAGTTA
*
1500478 TTCGGGGG
131 TTCGGGAG
*
1500486 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATAAAATAATGGAAGGCGCGCGCCC
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAA-G-GCGCGCCC
* * *
1500551 CCAGGAACGCGCTTTCACCACTTTACCAAGTC-CCATAAAAAATAATAGGTACTGACATGAATAT
64 CCAGGAACGCGCTTTCACCACTTTACCAAGTCTCC-TAAAAAATAATAGGTACTAACATAAATAG
*
1500615 TTCTTCGGGAG
128 TTATTCGGGAG
* * *
1500626 ACATGAGTGACATAATAGGGCAATGATAACATATTCGCTGACAAAATAATAGAAGGCACGCCCCC
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCC
1500691 AGGAACGCGCTTTCACCACTTT
66 AGGAACGCGCTTTCACCACTTT
1500713 GGGTACTGAT
Statistics
Matches: 206, Mismatches: 18, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
138 81 0.39
139 4 0.02
140 121 0.59
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (138 bp):
ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCC
AGGAACGCGCTTTCACCACTTTACCAAGTCTCCTAAAAAATAATAGGTACTAACATAAATAGTTA
TTCGGGAG
Found at i:1505192 original size:32 final size:32
Alignment explanation
Indices: 1505155--1505230 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 32
1505145 AATTAACAAG
* **
1505155 CAACGAGCATCGAATTTAATGAGCAACAAAAT
1 CAACGAGCAACGAATTTAACAAGCAACAAAAT
* * * *
1505187 TAACGAGTAACGAGTTTAACAAGCAACAAGAT
1 CAACGAGCAACGAATTTAACAAGCAACAAAAT
*
1505219 CAACGAGTAACG
1 CAACGAGCAACG
1505231 TGTTTAATGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.17
Consensus pattern (32 bp):
CAACGAGCAACGAATTTAACAAGCAACAAAAT
Found at i:1505205 original size:16 final size:16
Alignment explanation
Indices: 1505186--1505237 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1505176 AGCAACAAAA
1505186 TTAACGAGTAACGAGT
1 TTAACGAGTAACGAGT
* * * *
1505202 TTAACAAGCAACAAGA
1 TTAACGAGTAACGAGT
* *
1505218 TCAACGAGTAACGTGT
1 TTAACGAGTAACGAGT
1505234 TTAA
1 TTAA
1505238 TGAACAATAA
Statistics
Matches: 25, Mismatches: 11, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.23
Consensus pattern (16 bp):
TTAACGAGTAACGAGT
Found at i:1505236 original size:32 final size:32
Alignment explanation
Indices: 1505176--1505237 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1505166 GAATTTAATG
*
1505176 AGCAACAAAATTAACGAGTAACGAGTTTAACA
1 AGCAACAAAATCAACGAGTAACGAGTTTAACA
* *
1505208 AGCAACAAGATCAACGAGTAACGTGTTTAA
1 AGCAACAAAATCAACGAGTAACGAGTTTAA
1505238 TGAACAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.19
Consensus pattern (32 bp):
AGCAACAAAATCAACGAGTAACGAGTTTAACA
Found at i:1513761 original size:185 final size:184
Alignment explanation
Indices: 1513444--1513832 Score: 627
Period size: 185 Copynumber: 2.1 Consensus size: 184
1513434 AACCGAAATT
* ** *
1513444 AAATTTTAAATATATTATATATAACATATAGGCTCAGTTCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATAGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
*
1513509 TTTAAGATTCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
*
1513574 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
* * *
1513629 AAATATTAAATATATTATATATAATATATTGGCTTAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATAGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
* *
1513694 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
*
1513759 TTATTTTATAATTATATATTTTTTAAATTAATTATAAACTTTTTTTGAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
* * *
1513813 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
1513833 AATTAGAAAA
Statistics
Matches: 189, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
183 8 0.04
184 22 0.12
185 159 0.84
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATAGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
Found at i:1514720 original size:19 final size:19
Alignment explanation
Indices: 1514667--1514725 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
1514657 TATCATATAG
* *
1514667 TTTAGATTATTTATTAATA
1 TTTAGAATATATATTAATA
* *
1514686 TTTTA-AAAATAAATTAATA
1 -TTTAGAATATATATTAATA
1514705 TTTAGAATATATATT-ATA
1 TTTAGAATATATATTAATA
1514723 TTT
1 TTT
1514726 CAAAATAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
18 10 0.31
19 18 0.56
20 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTAGAATATATATTAATA
Found at i:1514720 original size:38 final size:38
Alignment explanation
Indices: 1514667--1514743 Score: 95
Period size: 38 Copynumber: 2.0 Consensus size: 38
1514657 TATCATATAG
* * *
1514667 TTTAGATTATTTATTAATATTT-TAAA-AATAAATTAATA
1 TTTAGAATATATATT-ATATTTCAAAATAATAAA-TAATA
1514705 TTTAGAATATATATTATATTTCAAAATAATAAATAATA
1 TTTAGAATATATATTATATTTCAAAATAATAAATAATA
1514743 T
1 T
1514744 AAATATATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 6 0.18
38 22 0.65
39 6 0.18
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (38 bp):
TTTAGAATATATATTATATTTCAAAATAATAAATAATA
Found at i:1514732 original size:19 final size:19
Alignment explanation
Indices: 1514678--1514732 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
1514668 TTAGATTATT
1514678 TATTAATATTTTAAAA-ATA
1 TATTAATA-TTTAAAATATA
* *
1514697 AATTAATATTTAGAATATA
1 TATTAATATTTAAAATATA
1514716 TATT-ATATTTCAAAATA
1 TATTAATATTT-AAAATA
1514733 ATAAATAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 12 0.40
19 18 0.60
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
TATTAATATTTAAAATATA
Found at i:1514752 original size:33 final size:33
Alignment explanation
Indices: 1514713--1514785 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
1514703 TATTTAGAAT
*
1514713 ATATATTATATT-TCAAAATAATAAATAATATAA
1 ATATATTATATTAT-AAAATAATAAATAACATAA
* * * *
1514746 ATATATTGTATTATAATATTATAAATAACATTA
1 ATATATTATATTATAAAATAATAAATAACATAA
1514779 ATATATT
1 ATATATT
1514786 TTTATATATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (33 bp):
ATATATTATATTATAAAATAATAAATAACATAA
Found at i:1514812 original size:30 final size:31
Alignment explanation
Indices: 1514733--1514818 Score: 93
Period size: 30 Copynumber: 2.7 Consensus size: 31
1514723 TTTCAAAATA
1514733 ATAAATAATATAAATATATTGTATTATAATATT
1 ATAAATAATATAAATATATT-T-TTATAATATT
* *
1514766 ATAAATAACATTAATATATTTTTAT-ATATT
1 ATAAATAATATAAATATATTTTTATAATATT
** * *
1514796 ATTTATAATAAAAATATTTTTTT
1 ATAAATAATATAAATATATTTTT
1514819 CAGAAAACCA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
30 22 0.49
31 4 0.09
32 1 0.02
33 18 0.40
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (31 bp):
ATAAATAATATAAATATATTTTTATAATATT
Found at i:1516438 original size:29 final size:29
Alignment explanation
Indices: 1516403--1516484 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
1516393 AAACTAAATT
* *
1516403 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
1516432 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
1516461 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1516485 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:1518075 original size:19 final size:19
Alignment explanation
Indices: 1518051--1518101 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1518041 GAAAATATTC
1518051 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1518070 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1518089 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1518102 TTTAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1518143 original size:65 final size:64
Alignment explanation
Indices: 1517945--1518152 Score: 230
Period size: 65 Copynumber: 3.2 Consensus size: 64
1517935 GCACCAAGTG
* * *
1517945 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCCTCGATGCATGG-CTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGGAC-TG
1518009 -
64 A
*
1518009 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGACT
1518071 GA
63 GA
* * *
1518073 GTGCATCGGTGCATGGAATGCATTCGATGTTT-AATTAATTCATCGATGCATCGATGCATGGACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGACT
1518137 GA
63 GA
*
1518139 TGCATCGGTGCATG
1 TGCATCGATGCATG
1518153 CCTTTGAATA
Statistics
Matches: 125, Mismatches: 8, Indels: 21
0.81 0.05 0.14
Matches are distributed among these distances:
63 8 0.06
64 49 0.39
65 64 0.51
66 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGACTGA
Found at i:1524564 original size:22 final size:21
Alignment explanation
Indices: 1524522--1524561 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1524512 GAGTTTGTTT
*
1524522 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1524543 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1524562 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1526506 original size:64 final size:63
Alignment explanation
Indices: 1526433--1526614 Score: 229
Period size: 64 Copynumber: 2.8 Consensus size: 63
1526423 TTGGAACACT
* ***
1526433 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATATCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATATCC
** * *
1526497 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATATCC
* * * *
1526561 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTT
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTT
1526615 AATTAATTCA
Statistics
Matches: 101, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
64 56 0.55
65 45 0.45
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATCC
Found at i:1526585 original size:19 final size:19
Alignment explanation
Indices: 1526561--1526611 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1526551 GAAAATATTC
1526561 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1526580 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1526599 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1526612 TTTAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1526587 original size:65 final size:65
Alignment explanation
Indices: 1526454--1526614 Score: 227
Period size: 65 Copynumber: 2.5 Consensus size: 65
1526444 TGCACCAAGT
* ***
1526454 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATATCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATATCCAGATGCATCGATGCATGGAGA
* *
1526518 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATATCCAGA-TGCATCGATGCATGGAG
1526582 A
65 A
* *
1526583 GTGCATCGGTGCATGGAATGCATTCGATGTTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTT
1526615 AATTAATTCA
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
64 38 0.44
65 48 0.56
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATATCCAGATGCATCGATGCATGGAGA
Found at i:1527474 original size:15 final size:15
Alignment explanation
Indices: 1527451--1527480 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1527441 ACGAGGCTGG
1527451 AATTACAACAACAAC
1 AATTACAACAACAAC
*
1527466 AATTCCAACAACAAC
1 AATTACAACAACAAC
1527481 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.13
Consensus pattern (15 bp):
AATTACAACAACAAC
Found at i:1530921 original size:29 final size:29
Alignment explanation
Indices: 1530846--1530928 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
1530836 CAAACTAAAT
* * *
1530846 TGATGTCATTACTTACACCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAAGTAA
*
1530875 AGATGTCATTGCTTACATCATTTAAGTAA
1 TGATGTCATTGCTTACATCATTTAAGTAA
1530904 TGATGTCATTGCTTACATCAATTTA
1 TGATGTCATTGCTTACATC-ATTTA
1530929 GTTAGGTAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 43 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.41
Consensus pattern (29 bp):
TGATGTCATTGCTTACATCATTTAAGTAA
Found at i:1536630 original size:2 final size:2
Alignment explanation
Indices: 1536623--1536651 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1536613 TTCCTGAAAA
1536623 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 A
1536652 GGACTTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1560741 original size:30 final size:30
Alignment explanation
Indices: 1560695--1560765 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
1560685 ACTTTTAAAA
* * *
1560695 ATTTATTATTAAGAGTCCAATTTTTTTAAT
1 ATTTGTTATTAAGAGTCCAATTTCTTCAAT
*
1560725 -TCTTGTTATTATGAGTCCAATTTCTTCAAT
1 AT-TTGTTATTAAGAGTCCAATTTCTTCAAT
1560755 ATTTGTTATTA
1 ATTTGTTATTA
1560766 GGGGTAGAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 1 0.03
30 33 0.94
31 1 0.03
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (30 bp):
ATTTGTTATTAAGAGTCCAATTTCTTCAAT
Found at i:1560916 original size:70 final size:70
Alignment explanation
Indices: 1560843--1560975 Score: 160
Period size: 70 Copynumber: 1.9 Consensus size: 70
1560833 TAGAAATTCA
* * * * *
1560843 TTTTTCAATATTTATTGTTAT-GAGCATACTCTTAAAATTTATTTTTTAAATATTTGTTATTAGA
1 TTTTTCAATACTTATT-ATATGGAG-ATACCCTTAAAATTTATTTTTTAAACATTTGTGATTAGA
1560907 GACCAAT
64 GACCAAT
* * * *
1560914 TTTTTCAATGCTTGTTATATGGAGTTACCCTTAAAATTTATTTTTTTAACATTTGTGATTAG
1 TTTTTCAATACTTATTATATGGAGATACCCTTAAAATTTATTTTTTAAACATTTGTGATTAG
1560976 GAACAACTAC
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
70 36 0.69
71 16 0.31
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (70 bp):
TTTTTCAATACTTATTATATGGAGATACCCTTAAAATTTATTTTTTAAACATTTGTGATTAGAGA
CCAAT
Found at i:1565872 original size:17 final size:17
Alignment explanation
Indices: 1565842--1565894 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
1565832 ATCAAAGAGT
*
1565842 TAGTTTAATTAATGAAC
1 TAGTTTAATCAATGAAC
* *
1565859 TAGTTAAATGAATGAAC
1 TAGTTTAATCAATGAAC
*
1565876 TAGTTTAATCAAAGAAC
1 TAGTTTAATCAATGAAC
1565893 TA
1 TA
1565895 ACTTTATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (17 bp):
TAGTTTAATCAATGAAC
Found at i:1567093 original size:27 final size:27
Alignment explanation
Indices: 1567063--1567117 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1567053 CTAATTACAT
1567063 TTTATACCTGGTTTTAATTGTGGTTGA
1 TTTATACCTGGTTTTAATTGTGGTTGA
*
1567090 TTTATGCCTGGTTTTAATTGTGGTTGA
1 TTTATACCTGGTTTTAATTGTGGTTGA
1567117 T
1 T
1567118 AACTGTGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.16, C:0.07, G:0.24, T:0.53
Consensus pattern (27 bp):
TTTATACCTGGTTTTAATTGTGGTTGA
Found at i:1585648 original size:2 final size:2
Alignment explanation
Indices: 1585641--1585677 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1585631 ATTTGATAAT
1585641 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1585678 GAATAAAGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1586314 original size:21 final size:20
Alignment explanation
Indices: 1586275--1586314 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1586265 TCAGTTTTGA
*
1586275 TTTATTTTATTATATAAATT
1 TTTATTTTATTATAAAAATT
*
1586295 TTTATTTTTATTTTAAAAAT
1 TTTA-TTTTATTATAAAAAT
1586315 CATACATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTATTTTATTATAAAAATT
Found at i:1590601 original size:3 final size:3
Alignment explanation
Indices: 1590593--1590618 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1590583 ACCTTCCACC
1590593 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1590619 AAAACAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1594589 original size:2 final size:2
Alignment explanation
Indices: 1594582--1594612 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1594572 GAGAAGTAGC
1594582 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 A
1594613 CACACACGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1595152 original size:42 final size:42
Alignment explanation
Indices: 1595105--1595191 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
1595095 CTTGATTCCA
* *
1595105 TATCATCTCCAACAACTTTTCTTTTTATGATTCTCGGATGTT
1 TATCATCTCCAACAACTTTGCTTTTTATGATTCTCGAATGTT
1595147 TATCATCTCCAACAACTTTGCTTTTTATGATTCTCGAATGTT
1 TATCATCTCCAACAACTTTGCTTTTTATGATTCTCGAATGTT
1595189 TAT
1 TAT
1595192 ATTTCAGAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (42 bp):
TATCATCTCCAACAACTTTGCTTTTTATGATTCTCGAATGTT
Found at i:1596560 original size:36 final size:31
Alignment explanation
Indices: 1596483--1596568 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 31
1596473 TTTAGCTGAC
* *
1596483 GAGTTTTCGAGTCCAGTCGAGCTTCATTTCA
1 GAGTTTTCGAGTCAAGTCGAGCTCCATTTCA
1596514 GAGTTTTCGAGTCAAGTCGAGCTCCATTTCA
1 GAGTTTTCGAGTCAAGTCGAGCTCCATTTCA
* *
1596545 GAGTTTTTGAGTCGAGTCGAGCTC
1 GAGTTTTCGAGTCAAGTCGAGCTC
1596569 AGTAATACTC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.34
Consensus pattern (31 bp):
GAGTTTTCGAGTCAAGTCGAGCTCCATTTCA
Found at i:1598870 original size:21 final size:20
Alignment explanation
Indices: 1598846--1598994 Score: 156
Period size: 20 Copynumber: 7.4 Consensus size: 20
1598836 CTCAATTTCC
* *
1598846 AAAATCGCAGCGTGAATTGT
1 AAAATCGCAACGTGAATAGT
* *
1598866 AAAAATCGTAACGTAAATAGT
1 -AAAATCGCAACGTGAATAGT
**
1598887 AAAAATAACAACGTGAATAGT
1 -AAAATCGCAACGTGAATAGT
*
1598908 AAAATCACAACGTGAATAGT
1 AAAATCGCAACGTGAATAGT
*
1598928 AAAATCGCAACGCGAATAGT
1 AAAATCGCAACGTGAATAGT
* *
1598948 AAAATCGCAATGCGAATAGT
1 AAAATCGCAACGTGAATAGT
* *
1598968 -AAATCGTAACGCGAATAGT
1 AAAATCGCAACGTGAATAGT
*
1598987 GAAATCGC
1 AAAATCGC
1598995 GTTGCGAATT
Statistics
Matches: 112, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
19 17 0.15
20 62 0.55
21 33 0.29
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGTGAATAGT
Found at i:1599016 original size:39 final size:39
Alignment explanation
Indices: 1598896--1599003 Score: 135
Period size: 39 Copynumber: 2.7 Consensus size: 39
1598886 TAAAAATAAC
* * * * *
1598896 AACGTGAATAGTAAAATCACAACGTGAATAGTAAAATCGC
1 AACGCGAATAGTAAAATCGCAATGCGAATAGT-AAATCGT
1598936 AACGCGAATAGTAAAATCGCAATGCGAATAGTAAATCGT
1 AACGCGAATAGTAAAATCGCAATGCGAATAGTAAATCGT
* **
1598975 AACGCGAATAGTGAAATCGCGTTGCGAAT
1 AACGCGAATAGTAAAATCGCAATGCGAAT
1599004 TTCAAATGGT
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 32 0.53
40 28 0.47
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (39 bp):
AACGCGAATAGTAAAATCGCAATGCGAATAGTAAATCGT
Found at i:1599467 original size:20 final size:20
Alignment explanation
Indices: 1599339--1599510 Score: 147
Period size: 20 Copynumber: 8.6 Consensus size: 20
1599329 ATATAGATTT
* *
1599339 GTTGCG-ATTTTACTATTCAC
1 GTTGCGAATTTGACTA-TCGC
* *
1599359 GTTGCGAAATTGGAGT-TCGC
1 GTTGCG-AATTTGACTATCGC
1599379 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
* * *
1599399 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGC
* * * *
1599419 GTTGTGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGC
1599439 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
*
1599459 GTTGCGAATTTGACT-TCTGT
1 GTTGCGAATTTGACTATC-GC
*
1599479 GTTGCG-ATTT-ACATATTCGA
1 GTTGCGAATTTGAC-TA-TCGC
1599499 GTTGCGAATTTG
1 GTTGCGAATTTG
1599511 GAAAATCGCA
Statistics
Matches: 127, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.02
19 14 0.11
20 100 0.79
21 6 0.05
22 5 0.04
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.42
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:1599503 original size:60 final size:60
Alignment explanation
Indices: 1599374--1599510 Score: 197
Period size: 60 Copynumber: 2.3 Consensus size: 60
1599364 GAAATTGGAG
* * *
1599374 TTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGTGAATTTGACT
1 TTCGAGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACT
* *
1599434 TTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCG-ATTT-ACAT
1 TTCGAGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGAC-T
1599493 ATTCGAGTTGCGAATTTG
1 -TTCGAGTTGCGAATTTG
1599511 GAAAATCGCA
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
58 2 0.03
59 5 0.07
60 62 0.90
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.43
Consensus pattern (60 bp):
TTCGAGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACT
Found at i:1599545 original size:20 final size:20
Alignment explanation
Indices: 1599479--1599546 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
1599469 TGACTTCTGT
*
1599479 GTTGCGATTTACATATTCGA
1 GTTGCGATTTACATATTCGC
** * *
1599499 GTTGCGAATTTGGAAAATCGC
1 GTTGCG-ATTTACATATTCGC
** *
1599520 AATGCGATTTATATATTCGC
1 GTTGCGATTTACATATTCGC
1599540 GTTGCGA
1 GTTGCGA
1599547 AATTGGAGTT
Statistics
Matches: 34, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 21 0.62
21 13 0.38
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACATATTCGC
Found at i:1603000 original size:2 final size:2
Alignment explanation
Indices: 1602993--1603021 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1602983 TTTCAAAATG
1602993 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1603022 TAATTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1607917 original size:17 final size:17
Alignment explanation
Indices: 1607889--1607938 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
1607879 TAATGATATT
*
1607889 TTTATGTAAAAAATTTAA
1 TTTAT-TAAAAAATTAAA
1607907 TTTATT-AAAAATTAAA
1 TTTATTAAAAAATTAAA
*
1607923 TTATAATAAAAAATTA
1 TT-TATTAAAAAATTA
1607939 CAATCATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 11 0.39
17 4 0.14
18 13 0.46
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTATTAAAAAATTAAA
Found at i:1607934 original size:18 final size:16
Alignment explanation
Indices: 1607895--1607938 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1607885 TATTTTTATG
*
1607895 TAAAAAATTTAATTTA
1 TAAAAAATTAAATTTA
*
1607911 TTAAAAATTAAATTATAA
1 TAAAAAATTAAATT-T-A
1607929 TAAAAAATTA
1 TAAAAAATTA
1607939 CAATCATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 12 0.52
17 1 0.04
18 10 0.43
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAAAATTAAATTTA
Found at i:1608749 original size:31 final size:31
Alignment explanation
Indices: 1608689--1608756 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1608679 TTACAATACA
* *
1608689 GTCCTCCAACATTTAATCTGTTAGCAATATG
1 GTCCCCCAACATTTAATCCGTTAGCAATATG
* * *
1608720 GTCCCCCAACATTTAGTCCGTTTGTAATATG
1 GTCCCCCAACATTTAATCCGTTAGCAATATG
1608751 GTCCCC
1 GTCCCC
1608757 AATGTAACTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.34
Consensus pattern (31 bp):
GTCCCCCAACATTTAATCCGTTAGCAATATG
Found at i:1610825 original size:31 final size:31
Alignment explanation
Indices: 1610765--1610832 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1610755 GGCTTTTTTT
* *
1610765 TATTAATATTTTTCTATGACTTGACATATTC
1 TATTAATATTTTTCTATGACATAACATATTC
* *
1610796 TATTAATATTTTAT-TATGACATAATATATTT
1 TATTAATATTTT-TCTATGACATAACATATTC
1610827 TATTAA
1 TATTAA
1610833 CATGACCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.53
Consensus pattern (31 bp):
TATTAATATTTTTCTATGACATAACATATTC
Found at i:1612020 original size:20 final size:21
Alignment explanation
Indices: 1611979--1612022 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1611969 GACCCGACCC
**
1611979 GACCGTTGACCATTGATTGTT
1 GACCGTTGACCATTGACCGTT
1612000 GACCG-TGACCATTGACCGTT
1 GACCGTTGACCATTGACCGTT
1612020 GAC
1 GAC
1612023 TTCCTTTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (21 bp):
GACCGTTGACCATTGACCGTT
Found at i:1623705 original size:2 final size:2
Alignment explanation
Indices: 1623698--1623746 Score: 66
Period size: 2 Copynumber: 25.0 Consensus size: 2
1623688 TAGTTGTACA
*
1623698 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AGT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
1623740 AT A- AT AT
1 AT AT AT AT
1623747 TTGTTGGGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 2 0.05
2 39 0.93
3 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1625017 original size:39 final size:39
Alignment explanation
Indices: 1624963--1625041 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
1624953 GAGTTTCTCT
1624963 TCAACTTTACTTAAATTTTGCTGTTGCATTCACTTATCA
1 TCAACTTTACTTAAATTTTGCTGTTGCATTCACTTATCA
1625002 TCAACTTTACTTAAATTTTGCTGTTGCATTCACTTATCA
1 TCAACTTTACTTAAATTTTGCTGTTGCATTCACTTATCA
1625041 T
1 T
1625042 GTCCCTGCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.47
Consensus pattern (39 bp):
TCAACTTTACTTAAATTTTGCTGTTGCATTCACTTATCA
Found at i:1628830 original size:16 final size:16
Alignment explanation
Indices: 1628809--1628842 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1628799 TTACTATTCA
*
1628809 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
1628825 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
1628841 CG
1 CG
1628843 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:1636715 original size:15 final size:16
Alignment explanation
Indices: 1636695--1636724 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1636685 TTTTTCTCAG
1636695 TAATTTTA-ATTTGAA
1 TAATTTTAGATTTGAA
1636710 TAATTTTAGATTTGA
1 TAATTTTAGATTTGA
1636725 GTTAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (16 bp):
TAATTTTAGATTTGAA
Found at i:1643897 original size:14 final size:14
Alignment explanation
Indices: 1643875--1643905 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1643865 CTTCCCATAG
*
1643875 ATGGTGTCACTTAA
1 ATGGCGTCACTTAA
1643889 ATGGCGTCACTTAA
1 ATGGCGTCACTTAA
1643903 ATG
1 ATG
1643906 AAAAAAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (14 bp):
ATGGCGTCACTTAA
Found at i:1647381 original size:24 final size:23
Alignment explanation
Indices: 1647290--1647383 Score: 67
Period size: 23 Copynumber: 4.3 Consensus size: 23
1647280 AAGTTAACTT
1647290 AAAAA-AATATTATAAATTTAACA
1 AAAAATAATA-TATAAATTTAACA
* *
1647313 AAAAATAATATAT--ATAT-A-T
1 AAAAATAATATATAAATTTAACA
* * *
1647332 ATATAT-ATATATGAATTTAACA
1 AAAAATAATATATAAATTTAACA
1647354 AAAAATAATATATAAATGTTAA-A
1 AAAAATAATATATAAAT-TTAACA
1647377 TAAAAAT
1 -AAAAAT
1647384 TTGAATTAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
18 6 0.11
19 4 0.07
20 4 0.07
21 4 0.07
22 4 0.07
23 18 0.33
24 14 0.26
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (23 bp):
AAAAATAATATATAAATTTAACA
Found at i:1649262 original size:539 final size:535
Alignment explanation
Indices: 1648230--1649301 Score: 1339
Period size: 539 Copynumber: 2.0 Consensus size: 535
1648220 TAATTTTCAT
* *
1648230 TTTAATCTTTATTTTTTATCAAACAACTTTTTAATGTTTTAATCTTTTCAAAACTATATACTTTT
1 TTTAATCCTTATTTTTTATCAAACAACTTTTTAATGTTTTAATATTTTCAAAACTATATACTTTT
* * * *
1648295 AGAGTAAATACACAAATGGTCTCCTGATTATAATATTGCTTTATTAAGTCCCTAAACTATTAAAA
66 AGAGGAAATACACAAATGGTCTCCTGACTATAATACTGATTTATTAAGTCCCTAAACTATT---A
* * * * *
1648360 GTTATAAAATGATTATTTGACTATAGAGTGTTGCTTTGTTGAGTCCATCAACTATTAAATGTTAT
128 -TTATAAAATGATCATTTGACAATAAAGTGTTGCTTTGTTGAGTCCATCAACTATTAAAAGTTAA
* * * * * * *
1648425 AAATCACCTTACTATTCATTATGTTTCAAACTCGTTCTTTACTGTTAAAAAATTGAATGTCGTAT
192 AAATCACCTGACAATTCAATATGTTCCAAACTCCTTCTTTACTGTTAAAAAATTGAATATAGTAT
* *
1648490 TGAGTTCGATGTTAACATGATGACTATGATATGACAGTCGTTTGAGATTTTGGGATTAGATTTTA
257 TGAGTTCGATGTTAACATGATGACTATAATATGACAGTCGTTTGAGATTTTGGGATCAGATTTTA
*
1648555 TCATATCACAATCAACAAGCTAACGTTAAGCTTATTTCGATAAAATTAGTAAAATTGAAAGTTTA
322 TCATATCACAATCAACAAGCTAACGTTAAGCTCATTTCGATAAAATTAGTAAAATTGAAAGTTTA
** * **
1648620 GTGGTATAAACGAGCTGGTACTTAAAATTTGGTGATATCTAATGTAGTTTTTATTCTTTTTGTTT
387 GTGGTATAAACGAGCTAATACTTAAAATTTGGTGAGATCTAATGTAGTTTACATTCTTTTTGTTT
* *** *
1648685 CGAGCTAAATGTTCATTTTGATACAGTAAATCTTGAGCTCCAAGGCATATTGTC-AAATAATTCT
452 CAAAAAAAATGTTCATTTTAATACAGTAAATCTTGAGCTCCAAGGCATATTGTCAAAATAATTCT
1648749 TAATATTTTATATTTTTAC
517 TAATATTTTATATTTTTAC
** * *
1648768 TTTAATCCTTATTTTTTTATCAAATGACTTTTTAATGTTTTAATATTTTCAAAACTATTTATTTT
1 TTTAATCCTTA-TTTTTTATCAAACAACTTTTTAATGTTTTAATATTTTCAAAACTATATACTTT
* * * *
1648833 TAGGGGAAAGTACACAAATGGTC-CTTTGACTATAGTACTGATTTATTAAGTCCCTCAACTA-T-
65 TAGAGGAAA-TACACAAATGGTCTC-CTGACTATAATACTGATTTATTAAGTCCCTAAACTATTA
* * * * *
1648895 TTATAAAATGGTCCTTTGACAATAAAGTGTTTCTTTGTTGAGTCCCTTAACTATTAAAAGTTACA
128 TTATAAAATGATCATTTGACAATAAAGTGTTGCTTTGTTGAGTCCATCAACTATTAAAAGTT--A
* *
1648960 AAAGGATCACCCTGACAATTCAATATGTTCCAAACTCC-TCTTTTTCTGTTAAAAAATTGATTAT
191 AAA--ATCA-CCTGACAATTCAATATGTTCCAAACTCCTTC-TTTACTGTTAAAAAATTGAATAT
* * * * * *
1649024 ATTTTTTAGTTGGATGTTAACATGATGACTATAATATGATAGTCGTTTGAGATTTTGGGATCATA
252 AGTATTGAGTTCGATGTTAACATGATGACTATAATATGACAGTCGTTTGAGATTTTGGGATCAGA
* * * * * * * *
1649089 TTTTATCATATCATAGTCAACAAGTTAATGTTTAA-CTCATTTTGATAAATTTGGTAAAGTTGAA
317 TTTTATCATATCACAATCAACAAGCTAACG-TTAAGCTCATTTCGATAAAATTAGTAAAATTGAA
* * ** *
1649153 AGTTTAGTGGTATAAACGAGCTAATACTTAAAGTTTGGTGGGATCTGGTGTAGTTTACCTTCTTT
381 AGTTTAGTGGTATAAACGAGCTAATACTTAAAATTTGGTGAGATCTAATGTAGTTTACATTCTTT
** *
1649218 TT-TGTTCAAAAAAAATGTTCATTTTAATATGGTAAATGTTGAGCTCCAAGGCATATTGTCAAAA
446 TTGT-TTCAAAAAAAATGTTCATTTTAATACAGTAAATCTTGAGCTCCAAGGCATATTGTC-AAA
1649282 ATAATTCTTAATATTTTATA
509 ATAATTCTTAATATTTTATA
1649302 AATTTTCACT
Statistics
Matches: 453, Mismatches: 68, Indels: 23
0.83 0.12 0.04
Matches are distributed among these distances:
534 53 0.12
536 3 0.01
538 17 0.04
539 311 0.69
540 47 0.10
541 22 0.05
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (535 bp):
TTTAATCCTTATTTTTTATCAAACAACTTTTTAATGTTTTAATATTTTCAAAACTATATACTTTT
AGAGGAAATACACAAATGGTCTCCTGACTATAATACTGATTTATTAAGTCCCTAAACTATTATTA
TAAAATGATCATTTGACAATAAAGTGTTGCTTTGTTGAGTCCATCAACTATTAAAAGTTAAAAAT
CACCTGACAATTCAATATGTTCCAAACTCCTTCTTTACTGTTAAAAAATTGAATATAGTATTGAG
TTCGATGTTAACATGATGACTATAATATGACAGTCGTTTGAGATTTTGGGATCAGATTTTATCAT
ATCACAATCAACAAGCTAACGTTAAGCTCATTTCGATAAAATTAGTAAAATTGAAAGTTTAGTGG
TATAAACGAGCTAATACTTAAAATTTGGTGAGATCTAATGTAGTTTACATTCTTTTTGTTTCAAA
AAAAATGTTCATTTTAATACAGTAAATCTTGAGCTCCAAGGCATATTGTCAAAATAATTCTTAAT
ATTTTATATTTTTAC
Found at i:1656059 original size:23 final size:23
Alignment explanation
Indices: 1656033--1656109 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
1656023 CCGAAGTTCT
1656033 ACATAGAAATATCCCGAAGGACC
1 ACATAGAAATATCCCGAAGGACC
* * *
1656056 ACATAGTATTATCCCGAATGACC
1 ACATAGAAATATCCCGAAGGACC
* * * *
1656079 ACGTAGAAATGTTCCAAAGGACC
1 ACATAGAAATATCCCGAAGGACC
*
1656102 ACGTAGAA
1 ACATAGAA
1656110 TTGTCTCGAA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.18
Consensus pattern (23 bp):
ACATAGAAATATCCCGAAGGACC
Found at i:1656086 original size:46 final size:46
Alignment explanation
Indices: 1656036--1656132 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 46
1656026 AAGTTCTACA
* *
1656036 TAGAAATATCCCGAAGGACCACATAGTATTATCCCGAATGACCACG
1 TAGAAATATCCCAAAGGACCACATAGAATTATCCCGAATGACCACG
* * * * * *
1656082 TAGAAATGTTCCAAAGGACCACGTAGAATTGTCTCGAATGACCGCG
1 TAGAAATATCCCAAAGGACCACATAGAATTATCCCGAATGACCACG
1656128 TAGAA
1 TAGAA
1656133 CCCTCAACTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (46 bp):
TAGAAATATCCCAAAGGACCACATAGAATTATCCCGAATGACCACG
Found at i:1656124 original size:23 final size:23
Alignment explanation
Indices: 1656047--1656132 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
1656037 AGAAATATCC
* * * *
1656047 CGAAGGACCACATAGTATTATCC
1 CGAAGGACCACGTAGAATTGTCT
* *
1656070 CGAATGACCACGTAGAAATGT-T
1 CGAAGGACCACGTAGAATTGTCT
*
1656092 CCAAAGGACCACGTAGAATTGTCT
1 -CGAAGGACCACGTAGAATTGTCT
* *
1656116 CGAATGACCGCGTAGAA
1 CGAAGGACCACGTAGAA
1656133 CCCTCAACTT
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
23 48 0.98
24 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (23 bp):
CGAAGGACCACGTAGAATTGTCT
Found at i:1661516 original size:24 final size:22
Alignment explanation
Indices: 1661467--1661508 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1661457 CCAGAATGTC
1661467 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
1661488 CAGGAGGGAACCGATTCCCCC
1 AAGGAGGGAACCGATACCCCC
1661509 CTAAAGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.29, C:0.36, G:0.29, T:0.07
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:1662436 original size:103 final size:103
Alignment explanation
Indices: 1662211--1662428 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
1662201 GTCGAGGGTC
1662211 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
1662276 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCGTAAGGAATGA
1662314 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
1662379 TTGATCCCTAGTATATGTATATGATTCGTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCGTAAGGAATGA
1662417 TATGTGGTCCTT
1 TATGTGGTCCTT
1662429 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCGTAAGGAATGA
Found at i:1662471 original size:23 final size:23
Alignment explanation
Indices: 1662438--1662559 Score: 131
Period size: 23 Copynumber: 5.3 Consensus size: 23
1662428 TATGGACATT
*
1662438 ATTATAT--GGCACTACGGTGTA
1 ATTATATGCGGCACTACGGTGCA
* *
1662459 ATTCTATGCGGCACTCCGGTGCA
1 ATTATATGCGGCACTACGGTGCA
**
1662482 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGCGGCACTACGGTGCA
* * *
1662506 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGCGGCACTACGGTGCA
* *
1662529 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGCGGCACTACGGTGCA
1662552 ATTATATG
1 ATTATATG
1662560 AGCTGTGGTG
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
21 6 0.07
23 57 0.70
24 19 0.23
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (23 bp):
ATTATATGCGGCACTACGGTGCA
Found at i:1662489 original size:47 final size:47
Alignment explanation
Indices: 1662435--1662559 Score: 198
Period size: 47 Copynumber: 2.7 Consensus size: 47
1662425 CCTTATGGAC
*
1662435 ATTATTATATGGCACTACGGTGTAATTCTATGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTATGCGGCACTCCGGTGCA
*
1662482 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTATGCGGCACTCCGGTGCA
* * *
1662529 ATTA-TATGTGGCACTTCGGTGCAATTATATG
1 ATTATTATATGGCACTACGGTGCAATTCTATG
1662560 AGCTGTGGTG
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
46 23 0.32
47 49 0.68
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTATGCGGCACTCCGGTGCA
Found at i:1665137 original size:2 final size:2
Alignment explanation
Indices: 1665130--1665161 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1665120 AATAAACTAT
1665130 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
1665162 GTTTAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1667984 original size:31 final size:31
Alignment explanation
Indices: 1667946--1668012 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1667936 TAAAAAAACA
* *
1667946 TAAGATTTGGTCATTTTCGTTTT-GTTTTAAT
1 TAAGATTTGATCACTTTC-TTTTCGTTTTAAT
*
1667977 TAAGATTTTATCACTTTCTTTTCGTTTTAAT
1 TAAGATTTGATCACTTTCTTTTCGTTTTAAT
1668008 TAAGA
1 TAAGA
1668013 CGTGGTCACT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (31 bp):
TAAGATTTGATCACTTTCTTTTCGTTTTAAT
Found at i:1668022 original size:31 final size:31
Alignment explanation
Indices: 1667953--1668022 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
1667943 ACATAAGATT
* **
1667953 TGGTCATTTTCGTTTTGTTTTAATTAAGATT
1 TGGTCACTTTCGTTTTGTTTTAATTAAGACG
**
1667984 TTATCACTTTC-TTTTCGTTTTAATTAAGACG
1 TGGTCACTTTCGTTTT-GTTTTAATTAAGACG
1668015 TGGTCACT
1 TGGTCACT
1668023 GAAGGCCAAC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.20, C:0.13, G:0.14, T:0.53
Consensus pattern (31 bp):
TGGTCACTTTCGTTTTGTTTTAATTAAGACG
Found at i:1668971 original size:30 final size:31
Alignment explanation
Indices: 1668900--1668972 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
1668890 CCTCATTTCC
*
1668900 AAGTGGCCAAAACTTAATAAACCGATAACGT
1 AAGTGACCAAAACTTAATAAACCGATAACGT
*
1668931 AAGT-ACCCAAAACTTAATAAACC-ATAATGT
1 AAGTGA-CCAAAACTTAATAAACCGATAACGT
1668961 AAGTGACCAAAA
1 AAGTGACCAAAA
1668973 GTGTACAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
30 16 0.42
31 22 0.58
ACGTcount: A:0.49, C:0.19, G:0.12, T:0.19
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAACCGATAACGT
Found at i:1674614 original size:3 final size:3
Alignment explanation
Indices: 1674600--1674686 Score: 113
Period size: 3 Copynumber: 29.3 Consensus size: 3
1674590 GTGGCATATA
*
1674600 AAG AAG ACG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * * * *
1674648 AAG AAG ATG GAG AAT CA- AAG AAG ATG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1674687 TGGAGAAAAC
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
2 1 0.01
3 71 0.99
ACGTcount: A:0.62, C:0.02, G:0.32, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:1676019 original size:15 final size:14
Alignment explanation
Indices: 1676001--1676043 Score: 61
Period size: 15 Copynumber: 3.0 Consensus size: 14
1675991 TAAATTTAGT
1676001 TTTTGAAATTTTAAA
1 TTTT-AAATTTTAAA
1676016 TTTTAAAATTTTAAA
1 TTTT-AAATTTTAAA
1676031 TTTT-AATTTTAAA
1 TTTTAAATTTTAAA
1676044 AATTAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 9 0.33
15 18 0.67
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TTTTAAATTTTAAA
Found at i:1676040 original size:6 final size:7
Alignment explanation
Indices: 1676001--1676043 Score: 61
Period size: 7 Copynumber: 6.0 Consensus size: 7
1675991 TAAATTTAGT
1676001 TTTTGAAA
1 TTTT-AAA
1676009 TTTTAAA
1 TTTTAAA
1676016 TTTTAAAA
1 TTTT-AAA
1676024 TTTTAAA
1 TTTTAAA
1676031 TTTT-AA
1 TTTTAAA
1676037 TTTTAAA
1 TTTTAAA
1676044 AATTAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.18
7 16 0.48
8 11 0.33
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (7 bp):
TTTTAAA
Found at i:1676047 original size:22 final size:23
Alignment explanation
Indices: 1676001--1676044 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 23
1675991 TAAATTTAGT
1676001 TTTTGAAATTTTAAATTTTAAAA
1 TTTTGAAATTTTAAATTTTAAAA
1676024 TTTT-AAATTTT-AATTTTAAAA
1 TTTTGAAATTTTAAATTTTAAAA
1676045 ATTAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 10 0.48
22 7 0.33
23 4 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTTGAAATTTTAAATTTTAAAA
Found at i:1677597 original size:16 final size:15
Alignment explanation
Indices: 1677572--1677601 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1677562 GGATGGTAAC
1677572 TTTCAAAAAATATAA
1 TTTCAAAAAATATAA
1677587 TTTCTAAAAAATATA
1 TTTC-AAAAAATATA
1677602 CTTACGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTCAAAAAATATAA
Found at i:1678330 original size:3 final size:3
Alignment explanation
Indices: 1678322--1678352 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1678312 GTGGATTAGC
1678322 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1678353 ATTATGTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1680087 original size:17 final size:18
Alignment explanation
Indices: 1680046--1680088 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1680036 AAATATATAA
1680046 ATTAATATTAATCATTATT
1 ATTAAT-TTAATCATTATT
* *
1680065 AATAATTTAATTA-TATT
1 ATTAATTTAATCATTATT
1680082 ATTAATT
1 ATTAATT
1680089 ATATTAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 10 0.48
18 6 0.29
19 5 0.24
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTAATTTAATCATTATT
Found at i:1680087 original size:30 final size:27
Alignment explanation
Indices: 1680046--1680112 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 27
1680036 AAATATATAA
*
1680046 ATTA-ATATTAATCATTATTAATAATTT
1 ATTATATATTAATCA-TATTAACAATTT
*
1680073 AATTATATTATTAATTATATTAACAATTT
1 -ATTATA-TATTAATCATATTAACAATTT
1680102 ATTATATATTA
1 ATTATATATTA
1680113 CTAAATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 5 0.14
28 10 0.29
29 12 0.34
30 8 0.23
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTATATATTAATCATATTAACAATTT
Found at i:1680153 original size:25 final size:24
Alignment explanation
Indices: 1680125--1680215 Score: 71
Period size: 25 Copynumber: 3.7 Consensus size: 24
1680115 AAATTAAAAA
1680125 ATATAATATCATATATTATTATAAT
1 ATATAATAT-ATATATTATTATAAT
* *
1680150 ATATCTAA-ATACATATTAATATAAT
1 ATA--TAATATATATATTATTATAAT
* *
1680175 AT-TAAAAATATAATATTATTAAAAT
1 ATAT-AATATAT-ATATTATTATAAT
*
1680200 -TATATTATATATATTA
1 ATATAATATATATATTA
1680216 AATATTTTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
22 1 0.02
23 8 0.15
24 9 0.17
25 30 0.57
26 2 0.04
27 3 0.06
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATAATATATATATTATTATAAT
Found at i:1680190 original size:19 final size:19
Alignment explanation
Indices: 1680166--1680217 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 19
1680156 AAATACATAT
1680166 TAATATAATATTAAAAATA
1 TAATATAATATTAAAAATA
*
1680185 TAATAT--TATTAAAATTA
1 TAATATAATATTAAAAATA
*
1680202 TATTATATATATTAAA
1 TAATATA-ATATTAAA
1680218 TATTTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 15 0.54
19 6 0.21
20 7 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATAATATTAAAAATA
Found at i:1680196 original size:17 final size:19
Alignment explanation
Indices: 1680117--1680217 Score: 68
Period size: 19 Copynumber: 5.3 Consensus size: 19
1680107 ATATTACTAA
*
1680117 ATTAAAAAATATAATATCAT
1 ATTAAAATATATAATAT-AT
**
1680137 A-TATTAT-TATAATATAT
1 ATTAAAATATATAATATAT
* *
1680154 -CTAAATACATATTAATATAAT
1 ATTAAA-ATATA-TAATAT-AT
1680175 ATTAAAA-ATATAATAT-T
1 ATTAAAATATATAATATAT
*
1680192 ATTAAAATTATATTATATAT
1 ATTAAAA-TATATAATATAT
1680212 ATTAAA
1 ATTAAA
1680218 TATTTTAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
17 12 0.19
18 9 0.14
19 19 0.30
20 17 0.27
21 3 0.05
22 4 0.06
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTAAAATATATAATATAT
Found at i:1680213 original size:28 final size:30
Alignment explanation
Indices: 1680163--1680231 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 30
1680153 TCTAAATACA
* *
1680163 TATTAATATAATATTAAAAATA-T-AATAT
1 TATTAAAATTATATTAAAAATATTAAATAT
* *
1680191 TATTAAAATTATATTATATATATTAAATAT
1 TATTAAAATTATATTAAAAATATTAAATAT
1680221 T-TTAATAATTA
1 TATTAA-AATTA
1680232 ATAAGTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 18 0.53
29 5 0.15
30 11 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TATTAAAATTATATTAAAAATATTAAATAT
Found at i:1680215 original size:48 final size:47
Alignment explanation
Indices: 1680162--1680254 Score: 109
Period size: 48 Copynumber: 1.9 Consensus size: 47
1680152 ATCTAAATAC
*
1680162 ATATTAATATAATATTAAAAATATAAT-A-TTATTAAAATTATATTATAT
1 ATATTAA-AT-ATATTAAAAAT-TAATAAGTTATTAAAATGATATTATAT
* *
1680210 ATATTAAATATTTTAATAATTAATAAGTTTATTAAAATGATATTA
1 ATATTAAATATATTAAAAATTAATAAG-TTATTAAAATGATATTA
1680255 AATTAATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
45 4 0.10
46 10 0.26
47 2 0.05
48 23 0.59
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (47 bp):
ATATTAAATATATTAAAAATTAATAAGTTATTAAAATGATATTATAT
Found at i:1680470 original size:42 final size:42
Alignment explanation
Indices: 1680390--1680478 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
1680380 TTATATTGAG
* *** *
1680390 AAAATCAATTACAACTATCGAACACTGGAAATTTTTTTTCGT
1 AAAATCAATTACAACTATCAAACACTGGAAAACATTTTTCGA
* *
1680432 AAAATTAATTACAACTATCAAACACTGTAAAACATTTTTCGA
1 AAAATCAATTACAACTATCAAACACTGGAAAACATTTTTCGA
1680474 AAAAT
1 AAAAT
1680479 ATTTTTCAGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.33
Consensus pattern (42 bp):
AAAATCAATTACAACTATCAAACACTGGAAAACATTTTTCGA
Found at i:1680669 original size:2 final size:2
Alignment explanation
Indices: 1680662--1680710 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1680652 ATTCGATGAA
1680662 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1680704 AT AT AT A
1 AT AT AT A
1680711 AAGAAAATGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1684244 original size:55 final size:55
Alignment explanation
Indices: 1684178--1684289 Score: 188
Period size: 55 Copynumber: 2.0 Consensus size: 55
1684168 ACCCCTCAAA
* * *
1684178 GTTAACATAACCTTTCAAATCTCATACATTTAAAGTAAGGAAATAGAACACACTT
1 GTTAACATAACCTTTCAAATCTCACACATTCAAAGAAAGGAAATAGAACACACTT
*
1684233 GTTAACATAACCTTTCAAATCTCACACATTCGAAGAAAGGAAATAGAACACACTT
1 GTTAACATAACCTTTCAAATCTCACACATTCAAAGAAAGGAAATAGAACACACTT
1684288 GT
1 GT
1684290 GTTGCTCTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.27
Consensus pattern (55 bp):
GTTAACATAACCTTTCAAATCTCACACATTCAAAGAAAGGAAATAGAACACACTT
Found at i:1685835 original size:27 final size:27
Alignment explanation
Indices: 1685792--1685844 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1685782 AATTTATGCA
1685792 TATTTTATATTTAGGTCACTGATTTAG
1 TATTTTATATTTAGGTCACTGATTTAG
* * *
1685819 TATTTTATGTTTTGGTCACTGGTTTA
1 TATTTTATATTTAGGTCACTGATTTA
1685845 TTTCTGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.08, G:0.17, T:0.55
Consensus pattern (27 bp):
TATTTTATATTTAGGTCACTGATTTAG
Found at i:1696982 original size:6 final size:7
Alignment explanation
Indices: 1696956--1697030 Score: 66
Period size: 7 Copynumber: 10.7 Consensus size: 7
1696946 AAGAAATGAA
*
1696956 AAAAAGG
1 AAAAATG
1696963 AAAAATGAG
1 AAAAAT--G
1696972 AAAAATG
1 AAAAATG
1696979 -AAAA-G
1 AAAAATG
*
1696984 AAAAAGG
1 AAAAATG
1696991 AAAAATG
1 AAAAATG
1696998 AAAAATG
1 AAAAATG
*
1697005 AAAAAATA
1 -AAAAATG
*
1697013 AAAAATA
1 AAAAATG
1697020 AAAAAT-
1 AAAAATG
1697026 AAAAA
1 AAAAA
1697031 AAATAAAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
5 1 0.02
6 13 0.22
7 33 0.55
8 6 0.10
9 7 0.12
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.09
Consensus pattern (7 bp):
AAAAATG
Found at i:1697010 original size:28 final size:29
Alignment explanation
Indices: 1696956--1697078 Score: 92
Period size: 28 Copynumber: 4.1 Consensus size: 29
1696946 AAGAAATGAA
1696956 AAAAAGGAAAAATGAGAAAAATG--AAAAG
1 AAAAAGGAAAAAT-AGAAAAATGAAAAAAG
*
1696984 AAAAAGGAAAAAT-GAAAAATGAAAAAATA
1 AAAAAGGAAAAATAGAAAAATGAAAAAA-G
** * *
1697013 AAAAATAAAAAATAAAAAAAATAAAAAAAG
1 AAAAAGGAAAAAT-AGAAAAATGAAAAAAG
*
1697043 AAGAAAGAGAAAAAATGATGAAAAAAG-AAAAAG
1 AA-AAAG-G-AAAAAT-A-GAAAAATGAAAAAAG
1697076 AAA
1 AAA
1697079 TAAAAGGGGG
Statistics
Matches: 74, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
26 8 0.11
28 17 0.23
29 11 0.15
30 2 0.03
31 15 0.20
32 1 0.01
33 15 0.20
34 5 0.07
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (29 bp):
AAAAAGGAAAAATAGAAAAATGAAAAAAG
Found at i:1697030 original size:35 final size:35
Alignment explanation
Indices: 1696956--1697030 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
1696946 AAGAAATGAA
* *
1696956 AAAAAGGAAAAATGAGAAAAATGAAAAGAAAAAGG
1 AAAAAGGAAAAATGAGAAAAATAAAAAGAAAAAAG
* * *
1696991 AAAAATGAAAAATGA-AAAAATAAAAAATAAAAAAT
1 AAAAAGGAAAAATGAGAAAAAT-AAAAAGAAAAAAG
1697026 AAAAA
1 AAAAA
1697031 AAATAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 6 0.18
35 28 0.82
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.09
Consensus pattern (35 bp):
AAAAAGGAAAAATGAGAAAAATAAAAAGAAAAAAG
Found at i:1697074 original size:7 final size:7
Alignment explanation
Indices: 1696979--1697057 Score: 56
Period size: 7 Copynumber: 11.6 Consensus size: 7
1696969 GAGAAAAATG
1696979 AAAAGAA
1 AAAAGAA
*
1696986 AAAGGAA
1 AAAAGAA
*
1696993 AAATGAA
1 AAAAGAA
*
1697000 AAATGAA
1 AAAAGAA
*
1697007 AAAATAA
1 AAAAGAA
*
1697014 AAAATAA
1 AAAAGAA
*
1697021 AAAATAA
1 AAAAGAA
1697028 AAAA-AA
1 AAAAGAA
1697034 TAAAA-AA
1 -AAAAGAA
*
1697041 AGAAG-A
1 AAAAGAA
*
1697047 AAGAGAA
1 AAAAGAA
1697054 AAAA
1 AAAA
1697058 TGATGAAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
6 9 0.15
7 52 0.85
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (7 bp):
AAAAGAA
Found at i:1700440 original size:21 final size:21
Alignment explanation
Indices: 1700414--1700458 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1700404 GATTTCTGGG
* *
1700414 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1700435 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1700456 CAA
1 CAA
1700459 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1700528 original size:23 final size:22
Alignment explanation
Indices: 1700484--1700528 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1700474 AATGCCAGAG
*
1700484 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
* *
1700506 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1700529 AAATGTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1701242 original size:62 final size:62
Alignment explanation
Indices: 1701124--1701246 Score: 203
Period size: 62 Copynumber: 2.0 Consensus size: 62
1701114 GGGTCGAGGG
* * *
1701124 TTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGTTTACCTAGGTTCTTCAGAACATATGGACTGT
1701186 TTACCTATGTTCTTCGGGACATATGGACTGTTTACCTAGGTTCTTCAGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGACATATGGACTGTTTACCTAGGTTCTTCAGAA-CATATGGACTG
1701247 GTCCTTCGGA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 56 0.98
63 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (62 bp):
TTACCTATGTTCTTCGGGACATATGGACTGTTTACCTAGGTTCTTCAGAACATATGGACTGT
Found at i:1701246 original size:31 final size:31
Alignment explanation
Indices: 1701124--1701231 Score: 207
Period size: 31 Copynumber: 3.5 Consensus size: 31
1701114 GGGTCGAGGG
1701124 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1701155 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1701186 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
1701217 TTACCTAGGTTCTTC
1 TTACCTATGTTCTTC
1701232 AGAATCTATG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:1703414 original size:9 final size:9
Alignment explanation
Indices: 1703400--1703490 Score: 55
Period size: 8 Copynumber: 11.3 Consensus size: 9
1703390 CTTAAAGAAG
1703400 AAATGAAAA
1 AAATGAAAA
1703409 AAATG--AA
1 AAATGAAAA
*
1703416 AAATGAGAA
1 AAATGAAAA
*
1703425 AAATGAGAA
1 AAATGAAAA
1703434 AAAT---AA
1 AAATGAAAA
1703440 AAA-GAAAA
1 AAATGAAAA
1703448 ATAA--AAAA
1 A-AATGAAAA
1703456 TAAATG-AAA
1 -AAATGAAAA
1703465 AAAT--AAA
1 AAATGAAAA
1703472 AAAT-AAAA
1 AAATGAAAA
1703480 AAAT-AAAA
1 AAATGAAAA
1703488 AAA
1 AAA
1703491 AATAAAAAAG
Statistics
Matches: 72, Mismatches: 0, Indels: 21
0.77 0.00 0.23
Matches are distributed among these distances:
6 5 0.07
7 14 0.19
8 27 0.38
9 26 0.36
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (9 bp):
AAATGAAAA
Found at i:1703447 original size:12 final size:11
Alignment explanation
Indices: 1703432--1703499 Score: 77
Period size: 12 Copynumber: 6.1 Consensus size: 11
1703422 GAAAAATGAG
1703432 AAAAATAAAAA
1 AAAAATAAAAA
1703443 GAAAAATAAAAA
1 -AAAAATAAAAA
*
1703455 ATAAATGAAAAA
1 AAAAAT-AAAAA
*
1703467 ATAAAA-AATAA
1 A-AAAATAAAAA
1703478 AAAAAT-AAAA
1 AAAAATAAAAA
1703488 AAAAATAAAAA
1 AAAAATAAAAA
1703499 A
1 A
1703500 GAAGAAAGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
10 13 0.27
11 15 0.31
12 17 0.35
13 3 0.06
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:1703454 original size:19 final size:19
Alignment explanation
Indices: 1703421--1703498 Score: 90
Period size: 19 Copynumber: 4.1 Consensus size: 19
1703411 ATGAAAAATG
1703421 AGAAAAATGAGAAAAATAAAA
1 AGAAAAAT-A-AAAAATAAAA
1703442 AGAAAAATAAAAAAT-AAA
1 AGAAAAATAAAAAATAAAA
*
1703460 TGAAAAAATAAAAAATAAAA
1 AG-AAAAATAAAAAATAAAA
1703480 A-AATAAA-AAAAAATAAAA
1 AGAA-AAATAAAAAATAAAA
1703498 A
1 A
1703499 AGAAGAAAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
18 18 0.35
19 22 0.42
20 4 0.08
21 8 0.15
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (19 bp):
AGAAAAATAAAAAATAAAA
Found at i:1703499 original size:7 final size:7
Alignment explanation
Indices: 1703406--1703489 Score: 62
Period size: 7 Copynumber: 10.9 Consensus size: 7
1703396 GAAGAAATGA
1703406 AAAAAAT
1 AAAAAAT
*
1703413 GAAAAAT
1 AAAAAAT
1703420 GAGAAAAAT
1 -A-AAAAAT
1703429 GAGAAAAAT
1 -A-AAAAAT
1703438 AAAAAGA-
1 AAAAA-AT
*
1703445 AAAATAAA
1 AAAA-AAT
1703453 AAATAAAT
1 AAA-AAAT
1703461 GAAAAAAT
1 -AAAAAAT
1703469 AAAAAAT
1 AAAAAAT
1703476 AAAAAAAT
1 -AAAAAAT
1703484 AAAAAA
1 AAAAAA
1703490 AAATAAAAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 16
0.78 0.04 0.19
Matches are distributed among these distances:
7 28 0.42
8 19 0.29
9 19 0.29
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:1703499 original size:19 final size:18
Alignment explanation
Indices: 1703432--1703499 Score: 93
Period size: 19 Copynumber: 3.7 Consensus size: 18
1703422 GAAAAATGAG
1703432 AAAAATAAAAAGAAAAATA
1 AAAAATAAAAA-AAAAATA
*
1703451 AAAAATAAATGAAAAAATA
1 AAAAATAAA-AAAAAAATA
1703470 AAAAATAAAAAAATAAA-A
1 AAAAATAAAAAAA-AAATA
1703488 AAAAATAAAAAA
1 AAAAATAAAAAA
1703500 GAAGAAAGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
18 16 0.36
19 28 0.62
20 1 0.02
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (18 bp):
AAAAATAAAAAAAAAATA
Found at i:1703513 original size:24 final size:23
Alignment explanation
Indices: 1703430--1703541 Score: 77
Period size: 22 Copynumber: 4.7 Consensus size: 23
1703420 GAGAAAAATG
*
1703430 AGAAAAATAAAAAGAAAAATAAAAA
1 AGAAAAA-GAAAA-AAAAATAAAAA
* * *
1703455 A-TAAATGAAAAAATAAA-AAATA
1 AGAAAAAGAAAAAA-AAATAAAAA
*
1703477 A-AAAAATAAAAAAAAATAAAAA
1 AGAAAAAGAAAAAAAAATAAAAA
*
1703499 AGAAGAAAGAGAAAAAATGATGAAAAA
1 AGAA-AAAGA-AAAAAA-AAT-AAAAA
*
1703526 AGAAAAAGAAATAAAA
1 AGAAAAAGAAAAAAAA
1703542 GGGGGGTTCA
Statistics
Matches: 68, Mismatches: 12, Indels: 15
0.72 0.13 0.16
Matches are distributed among these distances:
21 3 0.04
22 21 0.31
23 9 0.13
24 7 0.10
25 12 0.18
26 7 0.10
27 9 0.13
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (23 bp):
AGAAAAAGAAAAAAAAATAAAAA
Found at i:1703525 original size:44 final size:45
Alignment explanation
Indices: 1703406--1703541 Score: 126
Period size: 44 Copynumber: 3.1 Consensus size: 45
1703396 GAAGAAATGA
1703406 AAAAAATGAA-AAATGAG-AAAAATGA-G-AAAAATAAAAAGAAAAAT
1 AAAAAATGAAGAAA-GAGAAAAAATGATGAAAAAAT-AAAA-AAAAAT
* * *
1703450 AAAAAATAAATGAAA-A-AATAAAA-AATAAAAAAATAAAAAAAAAT
1 AAAAAATGAA-GAAAGAGAA-AAAATGATGAAAAAATAAAAAAAAAT
* *
1703494 AAAAAA-GAAGAAAGAGAAAAAATGATGAAAAAAGAAAAAGAAAT
1 AAAAAATGAAGAAAGAGAAAAAATGATGAAAAAATAAAAAAAAAT
1703538 AAAA
1 AAAA
1703542 GGGGGGTTCA
Statistics
Matches: 75, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
42 4 0.05
43 7 0.09
44 47 0.63
45 8 0.11
46 9 0.12
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (45 bp):
AAAAAATGAAGAAAGAGAAAAAATGATGAAAAAATAAAAAAAAAT
Found at i:1704870 original size:37 final size:37
Alignment explanation
Indices: 1704820--1704961 Score: 196
Period size: 37 Copynumber: 3.8 Consensus size: 37
1704810 ATAAGTTAAT
* * * * *
1704820 CTTAAACCTTCACGAAAAAGCAGTGAAGTAATTCAAA
1 CTTAAGCCTTCACGGAAGAGTAGTGAAGCAATTCAAA
1704857 CTTAAGCCTTCACGGAAGAGTAGTGAAGCAATTCAAA
1 CTTAAGCCTTCACGGAAGAGTAGTGAAGCAATTCAAA
* *
1704894 CTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC-AT
1 CTTAAGCCTTCACGGAAGAGTAGTGAAGCAATTCAAA
*
1704930 CTATAAGCCTTCAAGGAAGAGTAGTGAAGCAA
1 CT-TAAGCCTTCACGGAAGAGTAGTGAAGCAA
1704962 ACTCGTTTGT
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
36 3 0.03
37 93 0.97
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.21
Consensus pattern (37 bp):
CTTAAGCCTTCACGGAAGAGTAGTGAAGCAATTCAAA
Found at i:1705059 original size:55 final size:55
Alignment explanation
Indices: 1704988--1705346 Score: 390
Period size: 55 Copynumber: 6.6 Consensus size: 55
1704978 TTGAGTCATG
* * *
1704988 TACTCTCTGAATGAATAGAGAGCGGACCTGTTTGTTGAAGATTGTTCGAGTTTTA
1 TACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTTCTA
1705043 TACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGTTCGAGTTCTA
1 TACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-TGAAGATTGTTCGAGTTCTA
* *
1705098 TACTCTCTGAAGGAATAGAGAGCGGACCAGTTTGTTGAAGATTGTTCGAATTCTA
1 TACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTTCTA
* ** *
1705153 TACTCTCCGAAGGAATAGAGAGCATACCCGTTT-TATGAACATTGTTCGAGTTCTA
1 TACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-TGAAGATTGTTCGAGTTCTA
* * * * *
1705208 TATTCCCTGAACGG-ATAGGGAGCGGACCCATTTATTGAAGATTGTTCGAG-TCTTA
1 TACTCTCTGAA-GGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTTC-TA
* * * * ***
1705263 TACTCCCTGAATGAATAGGGAGCAGA--CGTTTGCCAAAGATTGTTCGAG-TCTTA
1 TACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTTC-TA
* * * * *
1705316 CACTCCCTGAAAGAATAGGGAGCAGACCCGT
1 TACTCTCTGAAGGAATAGAGAGCGGACCCGT
1705347 CATTTGAAGA
Statistics
Matches: 266, Mismatches: 29, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
53 46 0.17
54 5 0.02
55 211 0.79
56 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (55 bp):
TACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTTCTA
Found at i:1711801 original size:37 final size:36
Alignment explanation
Indices: 1711743--1711861 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
1711733 TCCCATTGCA
* *
1711743 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACC
*
1711779 ATTTTTCAAAGAAACATTTACCAAACTTAGAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1711815 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1711850 ATTTTTTCAAAG
1 A-TTTTTCAAAG
1711862 TTGGTTGCCA
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 34 0.45
36 14 0.18
37 28 0.37
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (36 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
Found at i:1711818 original size:21 final size:21
Alignment explanation
Indices: 1711793--1711853 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1711783 TTCAAAGAAA
1711793 CATTTACCAAACTTAGAAAAC
1 CATTTACCAAACTTAGAAAAC
*
1711814 CATTT-TC-AA---AG-AAA-
1 CATTTACCAAACTTAGAAAAC
*
1711828 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTAGAAAAC
1711849 CATTT
1 CATTT
1711854 TTTCAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 3 0.10
20 4 0.13
21 10 0.33
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.30
Consensus pattern (21 bp):
CATTTACCAAACTTAGAAAAC
Found at i:1716370 original size:37 final size:36
Alignment explanation
Indices: 1716312--1716430 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
1716302 TCCCATTACA
* *
1716312 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACC
1716348 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
*
1716384 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAATC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1716419 ATTTTTTCAAAG
1 A-TTTTTCAAAG
1716431 TTGGTTGCCA
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
35 34 0.44
36 14 0.18
37 29 0.38
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (36 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
Found at i:1716386 original size:21 final size:20
Alignment explanation
Indices: 1716359--1716422 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
1716349 TTTTTCAAAG
1716359 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
1716379 AAACCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
1716394 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
1716414 AAATCATTT
1 AAA-CATTT
1716423 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:1718158 original size:17 final size:17
Alignment explanation
Indices: 1718138--1718171 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1718128 AATTTTTGTT
*
1718138 ATAATTAATTTATTTTA
1 ATAATAAATTTATTTTA
1718155 ATAATAAATTTATTTTA
1 ATAATAAATTTATTTTA
1718172 TTTTATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATAATAAATTTATTTTA
Found at i:1719311 original size:13 final size:13
Alignment explanation
Indices: 1719293--1719318 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1719283 ATACTCCCTT
1719293 GAGTATCGGTACC
1 GAGTATCGGTACC
1719306 GAGTATCGGTACC
1 GAGTATCGGTACC
1719319 AAAATGACCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (13 bp):
GAGTATCGGTACC
Found at i:1728515 original size:14 final size:14
Alignment explanation
Indices: 1728496--1728526 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1728486 TTTTATTCAA
1728496 TAAAAATAATGATT
1 TAAAAATAATGATT
1728510 TAAAAATAATGATT
1 TAAAAATAATGATT
1728524 TAA
1 TAA
1728527 TTAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (14 bp):
TAAAAATAATGATT
Found at i:1728923 original size:2 final size:2
Alignment explanation
Indices: 1728916--1728941 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1728906 ATCTATCTAC
1728916 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1728942 GAATTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.