Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009623.1 Hibiscus syriacus cultivar Beakdansim tig00117012_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: 3488723
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 18
Found at i:1667521 original size:23 final size:22
Alignment explanation
Indices: 1667495--1667546 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
1667485 TTTCTATATA
*
1667495 TTTTTTTCATCATTTTTTCTTT
1 TTTTTTTTATCATTTTTTCTTT
* *
1667517 TTTTTTCTTTTTATTTTTTCTTT
1 TTTTTT-TTATCATTTTTTCTTT
*
1667540 TCTTTTT
1 TTTTTTT
1667547 CTTCTTCAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTTTTTATCATTTTTTCTTT
Found at i:1667528 original size:18 final size:19
Alignment explanation
Indices: 1667507--1667552 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1667497 TTTTTCATCA
*
1667507 TTTT-TTCTTTTTTTTTCT
1 TTTTATTCTTTTCTTTTCT
1667525 TTTTATT-TTTTCTTTTCT
1 TTTTATTCTTTTCTTTTCT
*
1667543 TTTTCTTCTT
1 TTTTATTCTT
1667553 CAAGCATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTTATTCTTTTCTTTTCT
Found at i:1667546 original size:13 final size:12
Alignment explanation
Indices: 1667514--1667552 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
1667504 TCATTTTTTC
1667514 TTTTTTTTTCTT
1 TTTTTTTTTCTT
1667526 TTTATTTTTTCTT
1 TTT-TTTTTTCTT
1667539 TTCTTTTTCTTCTT
1 TT-TTTTT-TTCTT
1667553 CAAGCATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.12
13 15 0.62
14 6 0.25
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:1671098 original size:9 final size:9
Alignment explanation
Indices: 1671084--1671108 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1671074 AGAAATAATG
1671084 AATGTAAAA
1 AATGTAAAA
1671093 AATGTAAAA
1 AATGTAAAA
1671102 AATGTAA
1 AATGTAA
1671109 GGTATAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (9 bp):
AATGTAAAA
Found at i:1672755 original size:21 final size:21
Alignment explanation
Indices: 1672731--1672799 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
1672721 TATGACTATA
1672731 TAAAATAATAAA-AATAATAT
1 TAAAATAATAAACAATAATAT
*
1672751 TTAAATATATAAACAAGTAA-AT
1 TAAAATA-ATAAACAA-TAATAT
1672773 TAAAATAATAAACAATAATA-
1 TAAAATAATAAACAATAATAT
1672793 -AAAATAA
1 TAAAATAA
1672800 AATTAGAACT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
19 7 0.16
20 9 0.21
21 14 0.33
22 10 0.23
23 3 0.07
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (21 bp):
TAAAATAATAAACAATAATAT
Found at i:1672791 original size:10 final size:9
Alignment explanation
Indices: 1672732--1672799 Score: 55
Period size: 9 Copynumber: 6.8 Consensus size: 9
1672722 ATGACTATAT
1672732 AAAATAATA
1 AAAATAATA
1672741 AAAATAATA
1 AAAATAATA
*
1672750 TTTAAATATATA
1 --AAAATA-ATA
*
1672762 AACAAGTAAATT
1 AA-AA-T-AATA
1672774 AAAATAATA
1 AAAATAATA
1672783 AACAATAATA
1 AA-AATAATA
1672793 AAAATAA
1 AAAATAA
1672800 AATTAGAACT
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
9 19 0.40
10 11 0.23
11 9 0.19
12 8 0.17
13 1 0.02
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.26
Consensus pattern (9 bp):
AAAATAATA
Found at i:1674146 original size:10 final size:9
Alignment explanation
Indices: 1674129--1674180 Score: 50
Period size: 10 Copynumber: 5.3 Consensus size: 9
1674119 AATAAATATT
1674129 AATAATAAA
1 AATAATAAA
1674138 AATATATAAA
1 AATA-ATAAA
*
1674148 AATAATCATAT
1 AATAAT-A-AA
1674159 AATAATAATA
1 AATAATAA-A
*
1674169 AATAAAAAA
1 AATAATAAA
1674178 AAT
1 AAT
1674181 CGGGACAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
9 11 0.31
10 18 0.50
11 7 0.19
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (9 bp):
AATAATAAA
Found at i:1674161 original size:27 final size:27
Alignment explanation
Indices: 1674130--1674181 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1674120 ATAAATATTA
* *
1674130 ATAATAAAAATATATAAAAATAATCAT
1 ATAATAAAAATAAATAAAAAAAATCAT
*
1674157 ATAATAATAATAAATAAAAAAAATC
1 ATAATAAAAATAAATAAAAAAAATC
1674182 GGGACAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (27 bp):
ATAATAAAAATAAATAAAAAAAATCAT
Found at i:1674696 original size:116 final size:112
Alignment explanation
Indices: 1674474--1675009 Score: 524
Period size: 116 Copynumber: 4.8 Consensus size: 112
1674464 CCTTCTAGAA
* * *
1674474 ATCAAGTGATGTA-TTGAGCAAAAGG-TGAAC-AA-GCTT-TCATTATGAACTTCTTCTTCCTTC
1 ATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTC
* *
1674534 TTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAA-GCTGATCC
66 TTCAGATGAGTTCTTCTCATTATGAAC--TTCCTGGAAAATGTTGATCC
* * * * *
1674582 ATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTC
1 ATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTC
* *
1674647 TTCAGATGACGAGTTCCTCTCATTATGAACTCTACCTGG-CAATGTTGATCC
66 TTCAGAT---GAGTTCTTCTCATTATGAACT-T-CCTGGAAAATGTTGATCC
* * * * *
1674698 ATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTT
1 ATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTC
1674763 TTCAGATGAGTTC-T-TCA-TATGAACTTCTCTGGAAAAGCTGATGCTGATCTCC
66 TTCAGATGAGTTCTTCTCATTATGAACTTC-CTGGAAAA--TG-T--TGA--TCC
* * *
1674815 TTC-TGTGATAGAATTT--GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-T
1 ATCAAGTGAT-GAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTT
* * *
1674876 CTTCAAATAAGTTCTTCTCATTATGAACTTTCTGGAAAAT-TTGATCC
65 CTTCAGATGAGTTCTTCTCATTATGAACTTCCTGGAAAATGTTGATCC
* * *
1674923 ATCGAA-TGATGAATTCAAACAAAAGGTTGAAC-AA-TC-T-TC-TTATAAACTTCTT-TT-CTT
1 ATC-AAGTGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTT
1674980 CTTCAGATGAGTTCTTCTCATTATGAACTT
65 CTTCAGATGAGTTCTTCTCATTATGAACTT
1675010 TAAACTGGTA
Statistics
Matches: 360, Mismatches: 39, Indels: 62
0.78 0.08 0.13
Matches are distributed among these distances:
103 1 0.00
104 31 0.09
105 11 0.03
106 2 0.01
107 1 0.00
108 25 0.07
109 22 0.06
110 31 0.09
111 4 0.01
112 7 0.02
113 37 0.10
114 14 0.04
115 48 0.13
116 107 0.30
117 19 0.05
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (112 bp):
ATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTC
TTCAGATGAGTTCTTCTCATTATGAACTTCCTGGAAAATGTTGATCC
Found at i:1674935 original size:225 final size:221
Alignment explanation
Indices: 1674492--1675010 Score: 605
Period size: 225 Copynumber: 2.3 Consensus size: 221
1674482 ATGTATTGAG
* *
1674492 CAAAAGG-TGAACAAGCTTTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 CAAAAGGTTGAACAATC-TTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTC-T-TCATTA
* * *
1674556 TGAACTTTTTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAGTTCT
63 TGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTT-AGCAAAAAGTTGAACAAATTCT
* *
1674621 TCTTATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCCTCTCATTATGAACTCTACCTGG
127 TCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAC-AGTTCCTCTCATTATGAACTCTACCTGG
*
1674686 CAATGTTGATCCATCAAATGATGAATTCAAA
191 AAATGTTGATCCATCAAATGATGAATTCAAA
*
1674717 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTTTTCAGATGAGTTCTTCA-T
1 CAAAAGGTTGAAC-AA-TC-T-TCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCATT
* ** *
1674781 ATGAAC-TTCTCTGGAAAAGCTGATGCTGATCTCCTTCTGTGATAGAATTT-GCAAAAGGTTGAA
62 ATGAACTTTCTCTGGAAAAGCTGAT-C-CA--T-C--AAGTGAT-GAATTTAGCAAAAAGTTGAA
* *
1674844 CAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAAAT-A-AGTTCTTCTCATTATGAACT-
119 CAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGACAGTTCCTCTCATTATGAACTC
* *
1674905 T-TCTGGAAAAT-TTGATCCATCGAATGATGAATTCAAA
184 TACCTGG-AAATGTTGATCCATCAAATGATGAATTCAAA
*
1674942 CAAAAGGTTGAACAATCTTC-TTATAAACTTC-T-TTTCTTCTTCAGATGAGTTCTTCTCATTAT
1 CAAAAGGTTGAACAATCTTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTC-T-TCATTAT
1675004 GAACTTT
64 GAACTTT
1675011 AAACTGGTAC
Statistics
Matches: 258, Mismatches: 19, Indels: 37
0.82 0.06 0.12
Matches are distributed among these distances:
218 19 0.07
219 2 0.01
220 13 0.05
221 9 0.03
222 3 0.01
223 2 0.01
224 2 0.01
225 66 0.26
226 17 0.07
227 25 0.10
228 4 0.02
229 37 0.14
230 9 0.03
231 40 0.16
232 5 0.02
233 5 0.02
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (221 bp):
CAAAAGGTTGAACAATCTTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCATTATGA
ACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTTAGCAAAAAGTTGAACAAATTCTTCTC
ATTATGAACTTCTTCTTCCTTCTTCAAATGACAGTTCCTCTCATTATGAACTCTACCTGGAAATG
TTGATCCATCAAATGATGAATTCAAA
Found at i:1675271 original size:204 final size:196
Alignment explanation
Indices: 1674876--1675283 Score: 719
Period size: 204 Copynumber: 2.0 Consensus size: 196
1674866 TCTTCTTCCT
1674876 CTTCAAATAAGTTCTTCTCATTATGAACTTTCTGGAAAATTTGATCCATCGAATGATGAATTCAA
1 CTTCAAATAAGTTCTTCTCATTATGAACTTTCTGGAAAATTTGATCCATCGAATGATGAATTCAA
1674941 ACAAAAGGTTGAACAATCTTCTTATAAACTTCTTTTCTTCTTCAGATGAGTTCTTCTCATTATGA
66 ACAAAAGGTTGAACAATCTTCTTATAAACTTCTTTTCTTCTTCAGATGAGTTCTTCTCATTATGA
1675006 ACTTTAAACTGGTACTGTGATCCATTGAATGATGTATTTAAATCTTTTCTAAAATCTTTAAAATT
131 ACTTTAAACTGGTACTGTGATCCATTGAATGATGTATTTAAATCTTTTCTAAAATCTTTAAAA-T
1675071 TC
195 TC
1675073 CTTCAAATAAGTTCTTCTCATTATGAACTTTCTGGAAAATTTGATCCATCGAATGATGAATTCAA
1 CTTCAAATAAGTTCTTCTCATTATGAACTTTCTGGAAAATTTGATCCATCGAATGATGAATTCAA
1675138 ACAAAAGGTTGAACAAATTCTTCTTATTATAAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTC
66 ACAAAAGGTTGAAC-AA-TCTTC---TTATAAACTTCTT-TT-CTTCTTCAGATGAGTTCTTCTC
1675203 ATTATGAACTTT-AACTGGTACTGTTGATCCATTGAATGATGTATTTAAATCTTTTCTAAAATCT
124 ATTATGAACTTTAAACTGGTACTG-TGATCCATTGAATGATGTATTTAAATCTTTTCTAAAATCT
1675267 TTAAAATTC
188 TTAAAATTC
1675276 CTGTCAAA
1 CT-TCAAA
1675284 ATTCAACATG
Statistics
Matches: 202, Mismatches: 0, Indels: 11
0.95 0.00 0.05
Matches are distributed among these distances:
197 79 0.39
198 2 0.01
199 5 0.02
202 13 0.06
203 18 0.09
204 85 0.42
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.40
Consensus pattern (196 bp):
CTTCAAATAAGTTCTTCTCATTATGAACTTTCTGGAAAATTTGATCCATCGAATGATGAATTCAA
ACAAAAGGTTGAACAATCTTCTTATAAACTTCTTTTCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTTTAAACTGGTACTGTGATCCATTGAATGATGTATTTAAATCTTTTCTAAAATCTTTAAAATT
C
Found at i:1676107 original size:114 final size:114
Alignment explanation
Indices: 1675947--1676277 Score: 518
Period size: 114 Copynumber: 2.9 Consensus size: 114
1675937 CATGCAGTTT
* * * * * * * * *
1675947 ATCTTTTAATTCCAATGATTGGTTCTGTGGTTCCTACCGAACCAGATCAGATGACTCAAAGAAAA
1 ATCTTTTAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
*
1676012 CTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAATTC
66 CTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATAAGCAAATTC
*
1676061 ATCTTTTAAATCTAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
1 ATCTTTTAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
*
1676126 CTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATAAGCAAATTT
66 CTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATAAGCAAATTC
* *
1676175 ATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAAATCAGATAACTCAAAGAACA
1 ATCTTTTAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
* *
1676240 CTTCTAGAAGATGCTTTTGGGTCTTCTTATTTCTACTA
66 CTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTA
1676278 CGAGAACGTA
Statistics
Matches: 200, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 200 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (114 bp):
ATCTTTTAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
CTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATAAGCAAATTC
Found at i:1676958 original size:6 final size:6
Alignment explanation
Indices: 1676942--1677017 Score: 55
Period size: 6 Copynumber: 11.7 Consensus size: 6
1676932 TGACCCCCTT
* * *
1676942 TTTTTC TTTTTTC TTTTTT TTTCTTC TATTTTTC TTCTTTC TTCTTC TTCTTC
1 TTTTTC -TTTTTC TTTTTC TTT-TTC --TTTTTC TT-TTTC TTTTTC TTTTTC
1676995 TTCTCTT- TTTTTC TTTTTC TTTT
1 TT-T-TTC TTTTTC TTTTTC TTTT
1677018 CTTCTTTTCA
Statistics
Matches: 58, Mismatches: 4, Indels: 15
0.75 0.05 0.19
Matches are distributed among these distances:
5 2 0.03
6 32 0.55
7 16 0.28
8 5 0.09
9 3 0.05
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:1676975 original size:21 final size:20
Alignment explanation
Indices: 1676940--1677025 Score: 84
Period size: 22 Copynumber: 4.0 Consensus size: 20
1676930 CTTGACCCCC
1676940 TTTTT-TTCTTTTTTCTTTT
1 TTTTTCTTCTTTTTTCTTTT
1676959 TTTTTCTTCTATTTTTCTTCTT
1 TTTTTCTTCT-TTTTTCTT-TT
*
1676981 TCTTCTTCTTCTTCTTCTCTTTT
1 T-TT-TTCTTCTT-TTTTCTTTT
*
1677004 TTTCTTTTTCTTTTCTTCTTTT
1 TTT-TTCTTCTTTT-TTCTTTT
1677026 CATTTTTTCT
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
19 5 0.09
20 4 0.07
21 10 0.18
22 19 0.33
23 6 0.11
24 13 0.23
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTCTTCTTTTTTCTTTT
Found at i:1676979 original size:3 final size:3
Alignment explanation
Indices: 1676973--1677023 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
1676963 TCTTCTATTT
* *
1676973 TTC TTC TTTC TTC TTC TTC TTC TTC -TC TT- TTT TTC TTT TTC TT-
1 TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1677016 TTC TTC TT
1 TTC TTC TT
1677024 TTCATTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
2 6 0.15
3 32 0.78
4 3 0.07
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (3 bp):
TTC
Found at i:1677018 original size:43 final size:41
Alignment explanation
Indices: 1676945--1677024 Score: 108
Period size: 43 Copynumber: 1.9 Consensus size: 41
1676935 CCCCCTTTTT
*
1676945 TTCTTTTTTCTTTTTTTTTCTTCTATTTTTCTTCTTTCTTC
1 TTCTTTTTTCTCTTTTTTTCTTCTATTTTTCTTCTTTCTTC
*
1676986 TTCTTCTTCTTCTCTTTTTTTCTT-TTTCTTTTCTTCTTT
1 TTCTT-TT-TTCTCTTTTTTTCTTCTAT-TTTTCTTCTTT
1677025 TCATTTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 5 0.15
42 4 0.12
43 25 0.74
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (41 bp):
TTCTTTTTTCTCTTTTTTTCTTCTATTTTTCTTCTTTCTTC
Found at i:1677019 original size:24 final size:24
Alignment explanation
Indices: 1676948--1677022 Score: 80
Period size: 30 Copynumber: 2.9 Consensus size: 24
1676938 CCTTTTTTTC
1676948 TTTTTTCTTTTT-TTTTCTTCTAT
1 TTTTTTCTTTTTCTTTTCTTCTAT
*
1676971 TTTTCTTCTTTCTTCTTCTTCTTCTTCTCT
1 TTTT-TTC--T-TT-TTCTT-TTCTTCTAT
1677001 TTTTTTCTTTTTCTTTTCTTCT
1 TTTTTTCTTTTTCTTTTCTTCT
1677023 TTTCATTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
23 4 0.09
24 10 0.23
25 5 0.11
26 3 0.07
27 3 0.07
28 2 0.05
29 5 0.11
30 12 0.27
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTTTCTTTTTCTTTTCTTCTAT
Found at i:1677032 original size:21 final size:19
Alignment explanation
Indices: 1676939--1677037 Score: 80
Period size: 21 Copynumber: 5.1 Consensus size: 19
1676929 TCTTGACCCC
1676939 CTTT-TTTTCTTTTTTCTT
1 CTTTCTTTTCTTTTTTCTT
* *
1676957 TTTTTTTCTTCTATTTTTCTT
1 CTTTCTT-TTCT-TTTTTCTT
1676978 CTTTCTTCTTCTTCTTCTTC-T
1 CTTTCTT-TTCTT-TT-TTCTT
1676999 CTTT-TTTTC-TTTTTCTT
1 CTTTCTTTTCTTTTTTCTT
*
1677016 TTCTTCTTTTCATTTTTTCTT
1 CT-TTCTTTTC-TTTTTTCTT
1677037 C
1 C
1677038 AAGCATAATA
Statistics
Matches: 66, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
16 3 0.05
17 4 0.06
18 6 0.09
19 10 0.15
20 7 0.11
21 33 0.50
22 3 0.05
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (19 bp):
CTTTCTTTTCTTTTTTCTT
Found at i:1677036 original size:43 final size:41
Alignment explanation
Indices: 1676941--1677037 Score: 106
Period size: 43 Copynumber: 2.2 Consensus size: 41
1676931 TTGACCCCCT
* *
1676941 TTTTTTCTTTTTTCTTTTTTTTTCTTCTATTTTTCTTCTTTC
1 TTTTTTC-TTCTTCTCTTTTTTTCTTCTATTTTTCTTCTTTC
*
1676983 TTCTTCTTCTTCTTCTCTTTTTTTCTT-TTTCTTTTCTTCTTTTC
1 TT-TT-TTCTTCTTCTCTTTTTTTCTTCTAT-TTTTCTTC-TTTC
1677027 ATTTTTTCTTC
1 -TTTTTTCTTC
1677038 AAGCATAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
42 4 0.09
43 32 0.68
44 9 0.19
45 2 0.04
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (41 bp):
TTTTTTCTTCTTCTCTTTTTTTCTTCTATTTTTCTTCTTTC
Found at i:1688337 original size:17 final size:18
Alignment explanation
Indices: 1688297--1688338 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1688287 AAATAATAAT
*
1688297 TTATATAAAATCAAATTA
1 TTATTTAAAATCAAATTA
**
1688315 AGATTTAAAAT-AAATTA
1 TTATTTAAAATCAAATTA
1688332 TTATTTA
1 TTATTTA
1688339 TTATATATAT
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
TTATTTAAAATCAAATTA
Found at i:1689775 original size:3 final size:3
Alignment explanation
Indices: 1689767--1689829 Score: 74
Period size: 3 Copynumber: 20.7 Consensus size: 3
1689757 GGCCTGTTTG
* * *
1689767 TAA TAA TAA TAA TAT TAA TAA TAA AAA TGTA TAA TAAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA T-AA TAA TAA TAA
1689813 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
1689830 TAAATAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 44 0.86
4 5 0.10
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1692741 original size:15 final size:15
Alignment explanation
Indices: 1692721--1692752 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1692711 TGCAATGAAT
1692721 AATGAATGTATGCAA
1 AATGAATGTATGCAA
1692736 AATGAATGTATGCAA
1 AATGAATGTATGCAA
1692751 AA
1 AA
1692753 GGTATTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:1696116 original size:28 final size:26
Alignment explanation
Indices: 1696061--1696118 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 26
1696051 TAAAAAAATT
*
1696061 AAAAAATAATATATATAAATATTATG
1 AAAAAATAATATATATAAAAATTATG
*
1696087 AAAATAATAAGTATATATAAAAATTTTG
1 AAAA-AATAA-TATATATAAAAATTATG
1696115 AAAA
1 AAAA
1696119 GAAATAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.14
27 5 0.18
28 19 0.68
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAAAATAATATATATAAAAATTATG
Found at i:1698408 original size:3 final size:3
Alignment explanation
Indices: 1698402--1698469 Score: 86
Period size: 3 Copynumber: 23.0 Consensus size: 3
1698392 AATTGTTTAT
* *
1698402 TAA TAA TAA TAA TAA TAA TAA TAA -AA TTA TAA -AA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1698448 TAAA TAA CAA TAA TAA TAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA
1698470 AAACAAATGG
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 4 0.07
3 49 0.88
4 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1698443 original size:25 final size:23
Alignment explanation
Indices: 1698404--1698469 Score: 80
Period size: 22 Copynumber: 2.8 Consensus size: 23
1698394 TTGTTTATTA
1698404 ATAATAATAATAATAATAATAAAATT
1 ATAA-AATAATAATAATAAT-AAA-T
*
1698430 ATAAAATAATAATATTAATAAAT
1 ATAAAATAATAATAATAATAAAT
*
1698453 A-ACAATAATAATAATAA
1 ATAAAATAATAATAATAA
1698470 AAACAAATGG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 14 0.38
23 2 0.05
24 3 0.08
25 14 0.38
26 4 0.11
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
ATAAAATAATAATAATAATAAAT
Found at i:1698477 original size:25 final size:24
Alignment explanation
Indices: 1698403--1698477 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 24
1698393 ATTGTTTATT
*
1698403 AATAATAATAATAATAATAATAAAA
1 AATAACAATAATAATAATAA-AAAA
* * *
1698428 TTATAA-AATAATAAT-AT-TAATA
1 -AATAACAATAATAATAATAAAAAA
1698450 AATAACAATAATAATAATAAAAACA
1 AATAACAATAATAATAATAAAAA-A
1698475 AAT
1 AAT
1698478 GGATGAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
21 4 0.10
22 12 0.31
23 2 0.05
24 4 0.10
25 13 0.33
26 4 0.10
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (24 bp):
AATAACAATAATAATAATAAAAAA
Found at i:1711859 original size:36 final size:37
Alignment explanation
Indices: 1711808--1711967 Score: 234
Period size: 38 Copynumber: 4.2 Consensus size: 37
1711798 AATATATAAT
1711808 TTTTAGAAAACGGATTTCGAAA-ATATATATTATATAG
1 TTTT-GAAAACGGATTTCGAAATATATATATTATATAG
1711845 TTTTGAAAACGGATTTCGGAAATATATATATTATATAG
1 TTTTGAAAACGGATTTC-GAAATATATATATTATATAG
*
1711883 TTTTGAAAACGG-TATTCGAAAATATATATATCATATAG
1 TTTTGAAAACGGAT-TTCG-AAATATATATATTATATAG
* *
1711921 CTTTGAAAACGGTTTTCGAAAATATATATATTATATAG
1 TTTTGAAAACGGATTTCG-AAATATATATATTATATAG
1711959 TTTTGAAAA
1 TTTTGAAAA
1711968 TATTTTGGAA
Statistics
Matches: 114, Mismatches: 4, Indels: 9
0.90 0.03 0.07
Matches are distributed among these distances:
36 13 0.11
37 10 0.09
38 90 0.79
39 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTTGAAAACGGATTTCGAAATATATATATTATATAG
Found at i:1711984 original size:38 final size:38
Alignment explanation
Indices: 1711808--1711988 Score: 219
Period size: 38 Copynumber: 4.8 Consensus size: 38
1711798 AATATATAAT
1711808 TTTTAGAAAACGGA-TTTCG-AAA-ATATATATTATATAG
1 TTTT-GAAAAC-GATTTTCGAAAATATATATATTATATAG
*
1711845 TTTTGAAAACGGA-TTTCGGAAATATATATATTATATAG
1 TTTTGAAAAC-GATTTTCGAAAATATATATATTATATAG
* * *
1711883 TTTTGAAAACGGTATTCGAAAATATATATATCATATAG
1 TTTTGAAAACGATTTTCGAAAATATATATATTATATAG
* *
1711921 CTTTGAAAACGGTTTTCGAAAATATATATATTATATAG
1 TTTTGAAAACGATTTTCGAAAATATATATATTATATAG
* *
1711959 TTTTGAAAA-TATTTTGGAAATATATATATA
1 TTTTGAAAACGATTTTCGAAA-ATATATATA
1711989 ATGAATATAT
Statistics
Matches: 129, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
36 14 0.11
37 16 0.12
38 99 0.77
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.40
Consensus pattern (38 bp):
TTTTGAAAACGATTTTCGAAAATATATATATTATATAG
Found at i:1712042 original size:53 final size:53
Alignment explanation
Indices: 1711942--1712051 Score: 127
Period size: 55 Copynumber: 2.1 Consensus size: 53
1711932 GTTTTCGAAA
* * *
1711942 ATATATATATTATATAGTTTTGAAAATATTTTGGAAATATATATATAATGAATAT
1 ATATATATATTATATAGTTTTAAAAAAATTTTGGAAATATACATATAAT--ATAT
* *
1711997 ATATATATATTATATGGTTTTAAAAACAATTTT-TAAA-A-ACATATAATATAT
1 ATATATATATTATATAGTTTTAAAAA-AATTTTGGAAATATACATATAATATAT
1712048 ATAT
1 ATAT
1712052 TTTCAAAAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
51 8 0.16
53 8 0.16
54 1 0.02
55 27 0.55
56 5 0.10
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (53 bp):
ATATATATATTATATAGTTTTAAAAAAATTTTGGAAATATACATATAATATAT
Found at i:1712089 original size:2 final size:2
Alignment explanation
Indices: 1712084--1712115 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1712074 TTTCCAAAAC
1712084 TA TA TA T- 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 T
1712116 TATTTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1716698 original size:21 final size:21
Alignment explanation
Indices: 1716668--1716715 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1716658 GCAGGGGTAC
* *
1716668 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
1716689 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
1716710 ATGCCA
1 ATGCCA
1716716 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:1716745 original size:21 final size:21
Alignment explanation
Indices: 1716719--1716812 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
1716709 TATGCCATCT
* *
1716719 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
1716740 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
1716761 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
1716782 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
1716803 CCGCAGGGTT
1 CCGCAGGGTT
1716813 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:1717389 original size:30 final size:31
Alignment explanation
Indices: 1717332--1717421 Score: 101
Period size: 31 Copynumber: 2.8 Consensus size: 31
1717322 AAATGTTTTT
* *
1717332 AAATACAAATTATATTATTCGAAATTTAAAA
1 AAATAAAAATAATATTATTCGAAATTTAAAA
1717363 AAATAAAAATAATATTATTC-AAATTTAAATTTA
1 AAATAAAAATAATATTATTCGAAATTTAAA---A
* * *
1717396 AAATATAAATTATAGTATTCGAAATT
1 AAATAAAAATAATATTATTCGAAATT
1717422 AACATTAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
30 9 0.18
31 18 0.36
33 18 0.36
34 5 0.10
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.38
Consensus pattern (31 bp):
AAATAAAAATAATATTATTCGAAATTTAAAA
Found at i:1717430 original size:33 final size:33
Alignment explanation
Indices: 1717332--1717430 Score: 116
Period size: 33 Copynumber: 3.1 Consensus size: 33
1717322 AAATGTTTTT
*
1717332 AAATACAAATTATATTATTCGAAATTTAAA--A
1 AAATAAAAATTATATTATTCGAAATTTAAATTA
*
1717363 AAATAAAAATAATATTATTC-AAATTTAAATTTA
1 AAATAAAAATTATATTATTCGAAATTTAAA-TTA
* *
1717396 AAATATAAATTATAGTATTCGAAA-TTAACATTA
1 AAATAAAAATTATATTATTCGAAATTTAA-ATTA
1717429 AA
1 AA
1717431 TTTCAACTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
30 9 0.16
31 18 0.31
33 27 0.47
34 4 0.07
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (33 bp):
AAATAAAAATTATATTATTCGAAATTTAAATTA
Found at i:1718158 original size:126 final size:126
Alignment explanation
Indices: 1717809--1718282 Score: 868
Period size: 123 Copynumber: 3.8 Consensus size: 126
1717799 TTTAAGTTAT
*
1717809 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
1717874 GCGTCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
1717935 ACCCCGAGGGACATGAATGACATAATAGGGCAATG---ATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
1717997 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
1718058 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
1718123 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTATTG--ATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
1718182 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1718247 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
1718283 CCGATTATAG
Statistics
Matches: 338, Mismatches: 7, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
123 120 0.36
124 111 0.33
126 107 0.32
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (126 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:1718362 original size:8 final size:8
Alignment explanation
Indices: 1718349--1718389 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1718339 TCACAATCTT
1718349 TCAAATTC
1 TCAAATTC
1718357 TCAAATTC
1 TCAAATTC
* *
1718365 CCAAACTC
1 TCAAATTC
1718373 T-AAATTC
1 TCAAATTC
1718380 TCAAATTC
1 TCAAATTC
1718388 TC
1 TC
1718390 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:1720269 original size:12 final size:11
Alignment explanation
Indices: 1720238--1720277 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
1720228 AAATACATAA
1720238 ATATATTTAAT
1 ATATATTTAAT
*
1720249 ATTTATTTAAT
1 ATATATTTAAT
1720260 ATAATATTTAAT
1 AT-ATATTTAAT
1720272 AT-TATT
1 ATATATT
1720278 AGTTATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 4 0.15
11 12 0.46
12 10 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATATATTTAAT
Found at i:1720338 original size:23 final size:23
Alignment explanation
Indices: 1720287--1720340 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 23
1720277 TAGTTATAAT
1720287 TTTTACAT--TATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
1720308 -TTTACATAATATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
1720330 TTTTACATAAT
1 TTTTACATAAT
1720341 TATTATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.23
22 13 0.43
23 10 0.33
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.39
Consensus pattern (23 bp):
TTTTACATAATATAATCGAAACA
Found at i:1720940 original size:31 final size:31
Alignment explanation
Indices: 1720869--1720944 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
1720859 CTTTTAAAAC
**
1720869 TTGCAATATAATCCCTCAACATTTAGTCCAT
1 TTGCAATATGGTCCCTCAACATTTAGTCCAT
*
1720900 TTGCAATATGGTCCCTTAACATTTAGAT-CAT
1 TTGCAATATGGTCCCTCAACATTTAG-TCCAT
1720931 TTGCAATATGGTCC
1 TTGCAATATGGTCC
1720945 TTGTAACTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 40 0.98
32 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (31 bp):
TTGCAATATGGTCCCTCAACATTTAGTCCAT
Found at i:1722367 original size:23 final size:21
Alignment explanation
Indices: 1722332--1722375 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
1722322 TTAATTATTT
1722332 AAAAAATTAAATAAAAATATAA
1 AAAAAATTAAATAAAAA-ATAA
*
1722354 AAAAACATTTAATAAAAAATAA
1 AAAAA-ATTAAATAAAAAATAA
1722376 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAATTAAATAAAAAATAA
Found at i:1727779 original size:36 final size:36
Alignment explanation
Indices: 1727722--1727861 Score: 235
Period size: 36 Copynumber: 3.9 Consensus size: 36
1727712 AGTTGAGTAT
**
1727722 TATCAGCTTTAATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
1727758 TATCAGCTTTGGTACACTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1727794 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* *
1727830 TATTAGCTTTGGTACATTCATGTATCAATGTT
1 TATCAGCTTTGGTACATTCGTGTATCAATGTT
1727862 CAGCACCATT
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 98 1.00
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:1730328 original size:74 final size:70
Alignment explanation
Indices: 1730210--1730464 Score: 232
Period size: 74 Copynumber: 3.5 Consensus size: 70
1730200 TTAATTAGGA
** * *
1730210 AATAACAATTAAAAATATATGAAAATATTTAAAATTATAGTTAATAAGTAATATTTAAAAATTAT
1 AATAA-AATTAAAAATATAAAAAAATA-TAAAAATTATAATTAATAAGTAA-A-TTAAAAATTAT
1730275 TTTTCCATT
62 TTTTCCATT
* *
1730284 AATAATAATTTAAAAATATAAAAAAATATAAAAATTATAATTAATAAATAAA--AATAAATCATT
1 AATAA-AA-TTAAAAATATAAAAAAATATAAAAATTATAATTAATAAGTAAATTAA-AAATTATT
1730347 TCTTCCATT
63 T-TTCCATT
* * * *** *
1730356 AACAAAATTGAAAATATAAAAAAATGTTGTGAATTATAATTAATAAGTAAAAGTTAAGAA-TATT
1 AATAAAATTAAAAATATAAAAAAAT-ATAAAAATTATAATTAATAAGT-AAA-TTAAAAATTATT
1730420 TTCTCCATT
63 TT-TCCATT
*
1730429 AATAAAAATTAAAAATAT--AAGAATATAAAAATTATA
1 AAT-AAAATTAAAAATATAAAAAAATATAAAAATTATA
1730465 GTAAATTATA
Statistics
Matches: 148, Mismatches: 23, Indels: 23
0.76 0.12 0.12
Matches are distributed among these distances:
70 19 0.13
71 35 0.24
72 20 0.14
73 13 0.09
74 42 0.28
75 19 0.13
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (70 bp):
AATAAAATTAAAAATATAAAAAAATATAAAAATTATAATTAATAAGTAAATTAAAAATTATTTTT
CCATT
Found at i:1730396 original size:71 final size:71
Alignment explanation
Indices: 1730268--1730464 Score: 190
Period size: 71 Copynumber: 2.8 Consensus size: 71
1730258 TAATATTTAA
* *
1730268 AAATTATTTTTCCATTAATAATAATTTAAAAATATAAAAAAATATAAAAATTATAATTAATAAAT
1 AAATCATTTTTCCATTAACAATAATTTAAAAATATAAAAAAATATAAAAATTATAATTAATAAAT
1730333 AAAAAT
66 AAAAAT
* * ***
1730339 AAATCATTTCTTCCATTAACAA-AA-TTGAAAATATAAAAAAATGTTGTGAATTATAATTAATAA
1 AAATCATTT-TTCCATTAACAATAATTTAAAAATATAAAAAAAT-ATAAAAATTATAATTAATAA
* *
1730402 GTAAAAGTT
64 ATAAAA-AT
* * *
1730411 AAGAAT-ATTTTCTCCATTAATAA-AAATTAAAAATAT--AAGAATATAAAAATTATA
1 -A-AATCATTTT-TCCATTAACAATAATTTAAAAATATAAAAAAATATAAAAATTATA
1730465 GTAAATTATA
Statistics
Matches: 103, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
70 17 0.17
71 39 0.38
72 18 0.17
73 17 0.17
74 12 0.12
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (71 bp):
AAATCATTTTTCCATTAACAATAATTTAAAAATATAAAAAAATATAAAAATTATAATTAATAAAT
AAAAAT
Found at i:1730986 original size:4 final size:4
Alignment explanation
Indices: 1730977--1731006 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1730967 ATTAGAGGAA
1730977 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1731007 GAAAAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1732842 original size:13 final size:13
Alignment explanation
Indices: 1732824--1732848 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1732814 TCATAACCCG
1732824 ACCCGACCCGTTT
1 ACCCGACCCGTTT
1732837 ACCCGACCCGTT
1 ACCCGACCCGTT
1732849 GACCGTTGAC
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:0.16, C:0.48, G:0.16, T:0.20
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:1733720 original size:17 final size:18
Alignment explanation
Indices: 1733695--1733730 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1733685 TTTTACAGAC
*
1733695 ATATTGATATG-ATAAAA
1 ATATGGATATGCATAAAA
1733712 ATATGGATATGCATAAAA
1 ATATGGATATGCATAAAA
1733730 A
1 A
1733731 ATGTTAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.53, C:0.03, G:0.14, T:0.31
Consensus pattern (18 bp):
ATATGGATATGCATAAAA
Found at i:1735334 original size:24 final size:24
Alignment explanation
Indices: 1735307--1735370 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
1735297 ATTTGAATTA
*
1735307 TGATCTGATACTTGACATGGATTT
1 TGATCTGATACTTGACATGGATTC
1735331 TGATCTGATA-TCTGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
* *
1735355 TAATATGATACTTGAC
1 TGATCTGATACTTGAC
1735371 TTGAATTATG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.03
24 33 0.94
25 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:1738390 original size:30 final size:30
Alignment explanation
Indices: 1738348--1738552 Score: 183
Period size: 30 Copynumber: 7.1 Consensus size: 30
1738338 GTAATTATAG
* *
1738348 TTTAGCCCTTTAAATTTTTATTTTTTCTAT
1 TTTAGTCCTTTAAATTTCTATTTTTTCTAT
* *
1738378 TTAAGTCCTTT-AA---CT-TTTTTTTTAT
1 TTTAGTCCTTTAAATTTCTATTTTTTCTAT
* **
1738403 TTTAGTCCTTTAACTTT-TATTTTAGCTAT
1 TTTAGTCCTTTAAATTTCTATTTTTTCTAT
* * **
1738432 TTTAGTCCTTTAACTTTCTATCTTAGCTAT
1 TTTAGTCCTTTAAATTTCTATTTTTTCTAT
* * *
1738462 TTTAGTCCCTTAAGTTTCTATTTTTTGTTAT
1 TTTAGTCCTTTAAATTTCTATTTTTT-CTAT
* *
1738493 TTTAGTCCTTTAAATGTCT-TTTTGT-TAT
1 TTTAGTCCTTTAAATTTCTATTTTTTCTAT
* *
1738521 TTTAGTCCTTTAAATGTCTATATTTTCTAT
1 TTTAGTCCTTTAAATTTCTATTTTTTCTAT
1738551 TT
1 TT
1738553 ATACCCTTAA
Statistics
Matches: 144, Mismatches: 22, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
25 19 0.13
26 2 0.01
28 23 0.16
29 30 0.21
30 51 0.35
31 19 0.13
ACGTcount: A:0.20, C:0.14, G:0.07, T:0.60
Consensus pattern (30 bp):
TTTAGTCCTTTAAATTTCTATTTTTTCTAT
Found at i:1738403 original size:25 final size:25
Alignment explanation
Indices: 1738368--1738533 Score: 125
Period size: 25 Copynumber: 5.9 Consensus size: 25
1738358 TAAATTTTTA
* *
1738368 TTTTTTCTATTTAAGTCCTTTAACT
1 TTTTTTTTATTTTAGTCCTTTAACT
1738393 TTTTTTTTATTTTAGTCCTTTAACT
1 TTTTTTTTATTTTAGTCCTTTAACT
1738418 TTTATTTTAGCTATTTTAGTCCTTTAACT
1 TTT-TTTT---TATTTTAGTCCTTTAACT
* *
1738447 TTCTATCTTAGCTATTTTAGTCCCTTAAGTTTCT
1 TT-T-T-TT--TTATTTTAGTCCTTTAA----CT
*
1738481 ATTTTTTGTTATTTTAGTCCTTTAAAT
1 -TTTTTT-TTATTTTAGTCCTTTAACT
1738508 GTCTTTTTGTTATTTTAGTCCTTTAA
1 -T-TTTTT-TTATTTTAGTCCTTTAA
1738534 ATGTCTATAT
Statistics
Matches: 119, Mismatches: 8, Indels: 25
0.78 0.05 0.16
Matches are distributed among these distances:
25 26 0.22
26 4 0.03
27 2 0.02
28 23 0.19
29 20 0.17
30 18 0.15
31 18 0.15
32 2 0.02
33 1 0.01
34 3 0.03
35 2 0.02
ACGTcount: A:0.19, C:0.14, G:0.07, T:0.60
Consensus pattern (25 bp):
TTTTTTTTATTTTAGTCCTTTAACT
Found at i:1738541 original size:59 final size:58
Alignment explanation
Indices: 1738348--1738552 Score: 215
Period size: 59 Copynumber: 3.6 Consensus size: 58
1738338 GTAATTATAG
* * *
1738348 TTTAGCCCTTTAAATTTTTATTTTTT-CTATTTAAGTCCTTTAACTT-TTTTT-TTAT
1 TTTAGTCCTTTAAATTTCTATTTTTTGCTATTTTAGTCCTTTAACTTCTTTTTGTTAT
* * * *
1738403 TTTAGTCCTTTAACTTT-TA-TTTTAGCTATTTTAGTCCTTTAACTTTCTATCTTAGCTAT
1 TTTAGTCCTTTAAATTTCTATTTTTTGCTATTTTAGTCCTTTAAC-TTCT-T-TTTGTTAT
* * * *
1738462 TTTAGTCCCTTAAGTTTCTATTTTTTGTTATTTTAGTCCTTTAAATGTCTTTTTGTTAT
1 TTTAGTCCTTTAAATTTCTATTTTTTGCTATTTTAGTCCTTTAACT-TCTTTTTGTTAT
* *
1738521 TTTAGTCCTTTAAATGTCTATATTTT-CTATTT
1 TTTAGTCCTTTAAATTTCTATTTTTTGCTATTT
1738553 ATACCCTTAA
Statistics
Matches: 123, Mismatches: 18, Indels: 15
0.79 0.12 0.10
Matches are distributed among these distances:
53 4 0.03
54 19 0.15
55 17 0.14
56 1 0.01
57 1 0.01
58 7 0.06
59 46 0.37
60 4 0.03
61 24 0.20
ACGTcount: A:0.20, C:0.14, G:0.07, T:0.60
Consensus pattern (58 bp):
TTTAGTCCTTTAAATTTCTATTTTTTGCTATTTTAGTCCTTTAACTTCTTTTTGTTAT
Found at i:1738541 original size:89 final size:89
Alignment explanation
Indices: 1738392--1738567 Score: 223
Period size: 89 Copynumber: 2.0 Consensus size: 89
1738382 GTCCTTTAAC
* * * * * *
1738392 TTTTTTTTTATTTTAGTCCTTTAACTTTTATTTTAGCTATTTTAGTCCTTTAACTTTCTATCTTA
1 TTTTTTGTTATTTTAGTCCTTTAAATTCTATTTTAGCTATTTTAGTCCTTTAAATGTCTATATTA
1738457 GCTATTT-TAGTCCCTTAAGTTTCTA
66 GCTATTTATA--CCCTTAAGTTTCTA
*
1738482 TTTTTTGTTATTTTAGTCCTTTAAATGTCT-TTTT-GTTATTTTAGTCCTTTAAATGTCTATATT
1 TTTTTTGTTATTTTAGTCCTTTAAAT-TCTATTTTAGCTATTTTAGTCCTTTAAATGTCTATATT
**
1738545 TTCTATTTATACCCTTAAGTTTC
65 AGCTATTTATACCCTTAAGTTTC
1738568 AGTTTTTACT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
88 12 0.16
89 31 0.41
90 30 0.40
91 2 0.03
ACGTcount: A:0.19, C:0.14, G:0.07, T:0.59
Consensus pattern (89 bp):
TTTTTTGTTATTTTAGTCCTTTAAATTCTATTTTAGCTATTTTAGTCCTTTAAATGTCTATATTA
GCTATTTATACCCTTAAGTTTCTA
Found at i:1738604 original size:118 final size:112
Alignment explanation
Indices: 1738348--1738624 Score: 267
Period size: 118 Copynumber: 2.4 Consensus size: 112
1738338 GTAATTATAG
* * *
1738348 TTTAGCCCTTTAAATTTTTATTTTTTCTATTTAAGTCCTTTAACTTTTTTTTTATTTTAGTCCTT
1 TTTAGCCCTTTAAGTTTATATTTTTTCTATTTAAGTCCTTTAAATTTTTTTTTATTTTAGTCCTT
* *
1738413 TAACTTTTATTTTAGCTATTTTAGTCCTTTAACTTTCTATCTTAGCTAT
66 TAAATTTTATTTTA-CTATTTTAG-CCCTTAACTTTCTATCTTAGCTAT
* * *
1738462 TTTAGTCCC-TTAAGTTTCTATTTTTTGTTATTTTAGTCCTTTAAATGTCTTTTTGTTATTTTAG
1 TTTAG-CCCTTTAAGTTTATATTTTTT-CTATTTAAGTCCTTTAAAT-T-TTTTT-TTATTTTAG
* * *
1738526 TCCTTTAAATGTCTATATTTT-CTATTTATA-CCCTTAAGTTTC-AGTTTTTA-CTGT
61 TCCTTTAAAT-T-T-TATTTTACTATTT-TAGCCCTTAACTTTCTA--TCTTAGCTAT
* * **
1738580 TTTAGCCCTTTAAGTTTATGTTTTTGCTATTTAAGTATTTTAAAT
1 TTTAGCCCTTTAAGTTTATATTTTTTCTATTTAAGTCCTTTAAAT
1738625 CGAATATGAT
Statistics
Matches: 134, Mismatches: 17, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
114 20 0.15
115 19 0.14
116 1 0.01
117 24 0.18
118 50 0.37
119 11 0.08
120 3 0.02
121 6 0.04
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.58
Consensus pattern (112 bp):
TTTAGCCCTTTAAGTTTATATTTTTTCTATTTAAGTCCTTTAAATTTTTTTTTATTTTAGTCCTT
TAAATTTTATTTTACTATTTTAGCCCTTAACTTTCTATCTTAGCTAT
Found at i:1740119 original size:3 final size:3
Alignment explanation
Indices: 1740107--1740143 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
1740097 ACATTATTTA
1740107 ATT A-T ATT ATT ATT ATT ATT ATT ATT AATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT A
1740144 CATTTTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1740126 original size:22 final size:22
Alignment explanation
Indices: 1740099--1740143 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1740089 TCTACAAAAC
1740099 ATTATT-TAATTATATTATTATT
1 ATTATTATAATTA-ATTATTATT
*
1740121 ATTATTATTATTAATTATTATT
1 ATTATTATAATTAATTATTATT
1740143 A
1 A
1740144 CATTTTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTATTATAATTAATTATTATT
Found at i:1740397 original size:34 final size:36
Alignment explanation
Indices: 1740353--1740454 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
1740343 TTTCGTCCTA
*
1740353 CTAGGATTCAAACTCCTAAAAATATGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
1740388 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
1740423 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
1740455 GTTCTACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 29 0.48
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:1740478 original size:37 final size:37
Alignment explanation
Indices: 1740350--1740488 Score: 158
Period size: 37 Copynumber: 3.8 Consensus size: 37
1740340 ATTTTTCGTC
* *
1740350 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1740387 -T--TAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
1740421 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
** * * *
1740458 CTACTATTATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
1740489 CCACAAGCAT
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
34 31 0.35
35 1 0.01
36 1 0.01
37 55 0.62
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:1741047 original size:16 final size:18
Alignment explanation
Indices: 1741026--1741060 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1741016 TTTACTCATT
1741026 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
1741042 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
1741060 T
1 T
1741061 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:1745768 original size:16 final size:16
Alignment explanation
Indices: 1745742--1745793 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
1745732 AGATCCAATC
1745742 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
1745757 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
* *
1745774 AA-AAAAAACAAAGAAA
1 AAGAACAAA-AAAGCAA
1745790 AAGA
1 AAGA
1745794 GAAACAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 8 0.26
16 18 0.58
17 5 0.16
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:1746503 original size:22 final size:22
Alignment explanation
Indices: 1746478--1746526 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1746468 CCATCAATCT
* *
1746478 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
1746500 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
1746522 TTTGA
1 TTTGA
1746527 CCAAACATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:1746966 original size:18 final size:18
Alignment explanation
Indices: 1746943--1746978 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1746933 TCAACATCAA
* *
1746943 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
1746961 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
1746979 GGATTTAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:1747501 original size:36 final size:36
Alignment explanation
Indices: 1747458--1747739 Score: 312
Period size: 36 Copynumber: 8.0 Consensus size: 36
1747448 ACTAGAAGAG
1747458 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
1747494 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
1747530 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1747566 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
1747602 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
** * ** * *
1747631 TTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
1747668 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
1747703 TTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1747740 ATCTTTGAAT
Statistics
Matches: 205, Mismatches: 29, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
35 6 0.03
36 142 0.69
37 34 0.17
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:1747501 original size:71 final size:73
Alignment explanation
Indices: 1747416--1747739 Score: 239
Period size: 72 Copynumber: 4.6 Consensus size: 73
1747406 GTTTTTCTTA
* * * * * *
1747416 AAACAAGA-TTTGTCTCGCTTGAGACCGTTTTCACTAG-AA-GAGTTTTGTCTCTCTTGAGACAG
1 AAACAA-ATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAG
1747478 TTTCCCTTG
65 TTTCCCTTG
* * *
1747487 AAACAAATTTTGTCTCTCTTGAGATAG-TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
1747551 TTCCCTTG
66 TTCCCTTG
* * * *
1747559 AAACAAATTTTGTCTCTCTTGAGACAG-TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACA-G
* *
1747615 TTTTCTTTG
65 TTTCCCTTG
** * ** * * * * *
1747624 AAACAAATTCCGTCTCCCTTGAGACAG-TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAAC-AAATTTCGTCTATCTTGAGACAG
*
1747688 TTTCTCTTG
65 TTTCCCTTG
* * *
1747697 AAAC-AATTTTCGTCTATCTTGAGACAG-TTTCCCTTGAAACAAA
1 AAACAAATTTT-GTCTCTCTTGAGACAGTTTTCACTAGAAACAAA
1747740 ATCTTTGAAT
Statistics
Matches: 203, Mismatches: 36, Indels: 27
0.76 0.14 0.10
Matches are distributed among these distances:
64 2 0.01
65 46 0.23
66 5 0.02
70 8 0.04
71 24 0.12
72 77 0.38
73 39 0.19
74 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (73 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
TTCCCTTG
Found at i:1747731 original size:138 final size:137
Alignment explanation
Indices: 1747478--1747802 Score: 454
Period size: 138 Copynumber: 2.4 Consensus size: 137
1747468 CTTGAGACAG
* *
1747478 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
*
1747543 GAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAACAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTT
*
1747608 GAATATG
131 GAATATA
* * ** * * * * *
1747615 TTTTCTTTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCT
* *
1747680 TGAGACAGTTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCT
65 TGAGACAGTTTCCCTTGAAACAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAATAT
*
1747744 TTGAATTTA
129 TTGAATATA
* * *
1747753 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1747803 CAAAATCTTC
Statistics
Matches: 161, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
137 48 0.30
138 113 0.70
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.39
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAACAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTT
GAATATA
Found at i:1747801 original size:65 final size:65
Alignment explanation
Indices: 1747697--1747871 Score: 217
Period size: 67 Copynumber: 2.6 Consensus size: 65
1747687 GTTTCTCTTG
** * **
1747697 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCT
1 AAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCT
1747761 A
65 A
* *
1747762 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
1747827 TA
64 TA
* * *
1747829 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
1747872 CAAATATCTT
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
65 25 0.26
66 12 0.13
67 31 0.33
68 27 0.28
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.37
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:1747802 original size:174 final size:168
Alignment explanation
Indices: 1747462--1747768 Score: 397
Period size: 174 Copynumber: 1.8 Consensus size: 168
1747452 GAAGAGTTTT
* *
1747462 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAAC
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
*
1747527 AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCC
66 AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA-----TATCTCTTGAGACAGTTTCCC
* * * *
1747592 TTGAAACAAAATATTTGAATATGTTTTCTTTGAAACAAATTCC
126 CTAAAACAAAATATTTGAACATGTTCTCTTTGAAACAAATTCC
** * *
1747635 GTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
1 GTCTCCCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
* *
1747700 CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA-ATCT-TTGA-ATTTA-TTTCCCCT
65 CAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAATATCTCTTGAGA--CAGTTTCCCCT
1747761 AAAACAAA
128 AAAACAAA
1747769 TTTTGTCTCC
Statistics
Matches: 120, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
166 1 0.01
167 18 0.15
168 4 0.03
173 25 0.21
174 72 0.60
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.39
Consensus pattern (168 bp):
GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAATATCTCTTGAGACAGTTTCCCCTAAA
ACAAAATATTTGAACATGTTCTCTTTGAAACAAATTCC
Found at i:1747831 original size:67 final size:67
Alignment explanation
Indices: 1747688--1747881 Score: 223
Period size: 65 Copynumber: 2.9 Consensus size: 67
1747678 CTTGAGACAG
* * ** * **
1747688 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAAT
1 TTTCCCTTAAAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAAT
1747750 TTA
65 TTA
* *
1747753 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
1747818 TA
66 TA
* * *
1747820 TTTCCCTTAAAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAACAAATATCTT
1 TTTCCCTTAAAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-ACAAA-ATCTT
1747882 TGAGATCGTT
Statistics
Matches: 109, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
65 31 0.28
66 8 0.07
67 29 0.27
68 31 0.28
69 5 0.05
70 5 0.05
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (67 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
TA
Found at i:1748697 original size:105 final size:105
Alignment explanation
Indices: 1748514--1749345 Score: 1298
Period size: 105 Copynumber: 8.0 Consensus size: 105
1748504 GCACTCGAGG
* * * * * *
1748514 CAACACAAGTTCAACGTCACAACGAAGGGACGGCTGGTTGTCAACAAACTACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
*
1748579 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
1748620 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* * *
1748685 GCCAATTTCAACTTTACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
1748725 CAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
1748790 GCCAATTTCAACTTTACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
1748830 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
1748895 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
1748935 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
1749000 GCCAATTTCAACTTCCCAACGAAGGCTATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
1749040 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1749105 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
1749145 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** *
1749205 TTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * * *
1749245 CAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCCCAGTTCCA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCA
* *
1749309 GAGCCAATTTCAACTTCACGACGGAGGATATTGGACT
64 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
1749346 TGGAACAATG
Statistics
Matches: 677, Mismatches: 42, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
99 2 0.00
100 81 0.12
101 3 0.00
102 3 0.00
103 4 0.01
104 3 0.00
105 506 0.75
106 75 0.11
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:1749937 original size:34 final size:36
Alignment explanation
Indices: 1749893--1749994 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
1749883 TTTCGTCCTA
*
1749893 CTAGGATTCAAACTCCTAAAAATATGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
1749928 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
1749963 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
1749995 GTTCTACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 29 0.48
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:1750018 original size:37 final size:37
Alignment explanation
Indices: 1749890--1750028 Score: 158
Period size: 37 Copynumber: 3.8 Consensus size: 37
1749880 ATTTTTCGTC
* *
1749890 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1749927 -T--TAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
1749961 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
** * * *
1749998 CTACTATTATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
1750029 CCACAAGCAT
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
34 31 0.35
35 1 0.01
36 1 0.01
37 55 0.62
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:1750447 original size:2 final size:2
Alignment explanation
Indices: 1750442--1750472 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1750432 TTAGTGTTAT
*
1750442 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1750473 TTCCTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1750601 original size:16 final size:18
Alignment explanation
Indices: 1750580--1750614 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1750570 TTTACTCATT
1750580 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
1750596 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
1750614 T
1 T
1750615 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:1750750 original size:16 final size:18
Alignment explanation
Indices: 1750710--1750750 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1750700 GTTATTGTTT
*
1750710 TTTATTTTATATATTCTA
1 TTTATTTTATATATTCAA
*
1750728 TTCATTTTATAT-TT-AA
1 TTTATTTTATATATTCAA
1750744 TTTATTT
1 TTTATTT
1750751 CTTACTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 7 0.35
17 2 0.10
18 11 0.55
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATTTTATATATTCAA
Found at i:1753070 original size:19 final size:18
Alignment explanation
Indices: 1753041--1753079 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
1753031 TGTTCCTTTT
1753041 GACACTCATTAATCCAAA
1 GACACTCATTAATCCAAA
1753059 GACACATCATTAATCCAAA
1 GACAC-TCATTAATCCAAA
1753078 GA
1 GA
1753080 GATGGCTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.46, C:0.26, G:0.08, T:0.21
Consensus pattern (18 bp):
GACACTCATTAATCCAAA
Found at i:1753541 original size:17 final size:17
Alignment explanation
Indices: 1753519--1753551 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1753509 TTAGTGTTCC
1753519 TTCAATT-TGTGCTTGTT
1 TTCAATTGTGT-CTTGTT
1753536 TTCAATTGTGTCTTGT
1 TTCAATTGTGTCTTGT
1753552 AATTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.58
Consensus pattern (17 bp):
TTCAATTGTGTCTTGTT
Found at i:1756752 original size:15 final size:15
Alignment explanation
Indices: 1756728--1756762 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1756718 GAAATTGTGA
*
1756728 GTGTTGTCTTTTGTT
1 GTGTTATCTTTTGTT
1756743 GTGTTATCTTTTGTT
1 GTGTTATCTTTTGTT
1756758 GTGTT
1 GTGTT
1756763 TTCAAAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.03, C:0.06, G:0.26, T:0.66
Consensus pattern (15 bp):
GTGTTATCTTTTGTT
Found at i:1757853 original size:12 final size:12
Alignment explanation
Indices: 1757837--1757879 Score: 70
Period size: 12 Copynumber: 3.6 Consensus size: 12
1757827 TCGATACATT
1757837 TTGCATT-TGCA
1 TTGCATTATGCA
1757848 TTTGCATTATGCA
1 -TTGCATTATGCA
1757861 TTGCATTATGCA
1 TTGCATTATGCA
1757873 TTGCATT
1 TTGCATT
1757880 TATTTAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 26 0.87
13 4 0.13
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (12 bp):
TTGCATTATGCA
Found at i:1757867 original size:5 final size:6
Alignment explanation
Indices: 1757836--1757880 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
1757826 ATCGATACAT
1757836 TTTGCA TTTGCA TTTGCA TTATGCA -TTGCA TTATGCA -TTGCA TTT
1 TTTGCA TTTGCA TTTGCA TT-TGCA TTTGCA TT-TGCA TTTGCA TTT
1757881 ATTTAAACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
5 8 0.23
6 19 0.54
7 8 0.23
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.49
Consensus pattern (6 bp):
TTTGCA
Found at i:1758439 original size:27 final size:27
Alignment explanation
Indices: 1758400--1758465 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
1758390 AATATCGAAT
1758400 GAATTATAGATTCTTTTAGTTCTTCAA
1 GAATTATAGATTCTTTTAGTTCTTCAA
* *
1758427 GAATTATATATTCTTTTAGTTCTTTAA
1 GAATTATAGATTCTTTTAGTTCTTCAA
1758454 GAATTATAGATT
1 GAATTATAGATT
1758466 TTTGACATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.50
Consensus pattern (27 bp):
GAATTATAGATTCTTTTAGTTCTTCAA
Found at i:1759271 original size:17 final size:14
Alignment explanation
Indices: 1759217--1759287 Score: 74
Period size: 15 Copynumber: 4.9 Consensus size: 14
1759207 CAAATCAAAG
1759217 CAAAGAG-AAAAA-
1 CAAAGAGAAAAAAT
1759229 CAAAGAGAAAAGAAT
1 CAAAGAGAAAA-AAT
* *
1759244 TAAAGAAAAAAAATT
1 CAAAGAGAAAAAA-T
1759259 GCAAAGAGGAAAAAAT
1 -CAAAGA-GAAAAAAT
1759275 CAAAGAGAAAAAA
1 CAAAGAGAAAAAA
1759288 AAAGCAAAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
12 7 0.14
13 3 0.06
14 11 0.22
15 16 0.33
16 6 0.12
17 6 0.12
ACGTcount: A:0.70, C:0.06, G:0.17, T:0.07
Consensus pattern (14 bp):
CAAAGAGAAAAAAT
Found at i:1759280 original size:31 final size:31
Alignment explanation
Indices: 1759208--1759319 Score: 95
Period size: 32 Copynumber: 3.5 Consensus size: 31
1759198 TGCAAAAATC
*
1759208 AAATCAAAGCAAAGAGAAAAA-CAAAGA-GAAA
1 AAATCAAAG-AAA-AAAAAAAGCAAAGAGGAAA
* **
1759239 AGAATTAAAGAAAAAAAATTGCAAAGAGGAAA
1 A-AATCAAAGAAAAAAAAAAGCAAAGAGGAAA
1759271 AAATCAAAGAGAAAAAAAAAGCAAAGGAAAGGAAA
1 AAATCAAAGA-AAAAAAAAAGCAAA-G--AGGAAA
1759306 AAA-CAAAAGAAAAA
1 AAATC-AAAGAAAAA
1759320 GCAAGGAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
30 4 0.06
31 18 0.27
32 24 0.36
33 1 0.02
34 5 0.08
35 14 0.21
ACGTcount: A:0.71, C:0.06, G:0.17, T:0.05
Consensus pattern (31 bp):
AAATCAAAGAAAAAAAAAAGCAAAGAGGAAA
Found at i:1759288 original size:17 final size:17
Alignment explanation
Indices: 1759247--1759319 Score: 57
Period size: 17 Copynumber: 4.4 Consensus size: 17
1759237 AAAGAATTAA
*
1759247 AGAAAAAAAATTGCAAAG
1 AGAAAAAAAAAT-CAAAG
*
1759265 AG--GAAAAAATCAAAG
1 AGAAAAAAAAATCAAAG
*
1759280 AGAAAAAAAAAGCAAAG
1 AGAAAAAAAAATCAAAG
1759297 -GAAAGGAAAAAA-CAAA-
1 AGAAA--AAAAAATCAAAG
1759313 AGAAAAA
1 AGAAAAA
1759320 GCAAGGAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
15 9 0.20
16 10 0.22
17 19 0.41
18 8 0.17
ACGTcount: A:0.73, C:0.05, G:0.18, T:0.04
Consensus pattern (17 bp):
AGAAAAAAAAATCAAAG
Found at i:1759289 original size:33 final size:32
Alignment explanation
Indices: 1759245--1759319 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
1759235 GAAAAGAATT
*
1759245 AAAGAAAAAAAATTGCAAA-G-AGGAAAAAATCA
1 AAAGAAAAAAAA-AGCAAAGGAAGGAAAAAA-CA
1759277 AAGAGAAAAAAAAAGCAAAGGAAAGGAAAAAACA
1 AA-AGAAAAAAAAAGCAAAGG-AAGGAAAAAACA
1759311 AAAGAAAAA
1 AAAGAAAAA
1759320 GCAAGGAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
32 7 0.18
33 18 0.47
34 4 0.11
35 9 0.24
ACGTcount: A:0.73, C:0.05, G:0.17, T:0.04
Consensus pattern (32 bp):
AAAGAAAAAAAAAGCAAAGGAAGGAAAAAACA
Found at i:1759313 original size:23 final size:22
Alignment explanation
Indices: 1759282--1759330 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
1759272 AATCAAAGAG
* *
1759282 AAAAAAAAAGCAAAGGAAAGGA
1 AAAAAAAAAGAAAAAGAAAGGA
*
1759304 AAAAACAAAAGAAAAAGCAAGGA
1 AAAAA-AAAAGAAAAAGAAAGGA
1759327 AAAA
1 AAAA
1759331 TAAGACAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAGAAAAAGAAAGGA
Found at i:1760401 original size:33 final size:34
Alignment explanation
Indices: 1760359--1760427 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 34
1760349 AAACCAGTGA
* *
1760359 TGAAGCAATCAACAA-CGAAT-ATTGGGGCATCTT
1 TGAAGCAATCAA-AATAGAATGATTGGGGAATCTT
1760392 TGAAGCAATCAAAATAGAATGATTGGGGAATCTT
1 TGAAGCAATCAAAATAGAATGATTGGGGAATCTT
1760426 TG
1 TG
1760428 GGGATTCAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 2 0.06
33 16 0.50
34 14 0.44
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (34 bp):
TGAAGCAATCAAAATAGAATGATTGGGGAATCTT
Found at i:1760652 original size:33 final size:34
Alignment explanation
Indices: 1760615--1760703 Score: 108
Period size: 36 Copynumber: 2.6 Consensus size: 34
1760605 AATCTTTGAA
* *
1760615 TCTGTTTCAGTTTAAACAAAA-AAAATCATAGAG
1 TCTGTTTCACTTGAAACAAAACAAAATCATAGAG
* *
1760648 TCTGTTTCACTTGAAACAAAATGCAAAATCTTTGAG
1 TCTGTTTCACTTGAAACAAAA--CAAAATCATAGAG
*
1760684 TCTGTTTCCCTTGAAACAAA
1 TCTGTTTCACTTGAAACAAA
1760704 GTGTTATCTC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
33 19 0.40
36 29 0.60
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (34 bp):
TCTGTTTCACTTGAAACAAAACAAAATCATAGAG
Found at i:1760685 original size:36 final size:33
Alignment explanation
Indices: 1760602--1760703 Score: 123
Period size: 33 Copynumber: 3.0 Consensus size: 33
1760592 ATTTCTTTTG
* * *
1760602 AAAAATCTTTGAATCTGTTTCAGTTTAAACAAA
1 AAAAATCTTTGAGTCTGTTTCACTTGAAACAAA
* *
1760635 AAAAATCATAGAGTCTGTTTCACTTGAAACAAA
1 AAAAATCTTTGAGTCTGTTTCACTTGAAACAAA
*
1760668 ATGCAAAATCTTTGAGTCTGTTTCCCTTGAAACAAA
1 A---AAAATCTTTGAGTCTGTTTCACTTGAAACAAA
1760704 GTGTTATCTC
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
33 29 0.50
36 29 0.50
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (33 bp):
AAAAATCTTTGAGTCTGTTTCACTTGAAACAAA
Found at i:1760818 original size:97 final size:98
Alignment explanation
Indices: 1760645--1760851 Score: 244
Period size: 97 Copynumber: 2.1 Consensus size: 98
1760635 AAAAATCATA
*** *
1760645 GAGTCTGTTTCACTTGAAACAAAATGCAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTGTTA
1 GAGTCTGTTTCACTTGAAACAAAAAAAAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAG-ATTA
*
1760710 TCTCTCTTGAGACAGTTT-TCTTGAGAAATATTT
65 TCTCTCTTGAGACAGTTTCTCTTGAAAAATATTT
*
1760743 GAGTCT-TTTCACTTGAAACAAAACAAAAAAAATCTTTGAGTCTGTTT-CTTTGGTAAA-AAA-A
1 GAGTCTGTTTCACTTGAAAC-AAA-AAAAAAAATCTTTGAGTCTGTTTCCCTT-G-AAACAAAGA
* * * *
1760804 TTGTCTCTTTTGAGACAGTTTCTTTTGAAAAATCTTT
62 TTATCTCTCTTGAGACAGTTTCTCTTGAAAAATATTT
1760841 GAGTCTGTTTC
1 GAGTCTGTTTC
1760852 TTTGGAATTT
Statistics
Matches: 93, Mismatches: 10, Indels: 11
0.82 0.09 0.10
Matches are distributed among these distances:
97 32 0.34
98 30 0.32
99 28 0.30
100 3 0.03
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (98 bp):
GAGTCTGTTTCACTTGAAACAAAAAAAAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGATTAT
CTCTCTTGAGACAGTTTCTCTTGAAAAATATTT
Found at i:1760923 original size:30 final size:30
Alignment explanation
Indices: 1760887--1760943 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1760877 TGAGACAGTA
* *
1760887 TCTTTGATTTTGTTTCTATTGAAACAAAAG
1 TCTTTGAGTCTGTTTCTATTGAAACAAAAG
1760917 TCTTTGAGTCTGTTTCTATTGAAACAA
1 TCTTTGAGTCTGTTTCTATTGAAACAA
1760944 TAAATCATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (30 bp):
TCTTTGAGTCTGTTTCTATTGAAACAAAAG
Found at i:1760960 original size:34 final size:30
Alignment explanation
Indices: 1760886--1760949 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
1760876 TTGAGACAGT
* *
1760886 ATCTTTGATTTTGTTTCTATTGAAACAAAA
1 ATCTTTGAGTCTGTTTCTATTGAAACAAAA
*
1760916 GTCTTTGAGTCTGTTTCTATTGAAACAATAA
1 ATCTTTGAGTCTGTTTCTATTGAAACAA-AA
1760947 ATC
1 ATC
1760950 ATCTTTGAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (30 bp):
ATCTTTGAGTCTGTTTCTATTGAAACAAAA
Found at i:1761232 original size:65 final size:62
Alignment explanation
Indices: 1761051--1761222 Score: 229
Period size: 65 Copynumber: 2.7 Consensus size: 62
1761041 AATGTTGTCG
* *
1761051 CTTGAGACAATTTCTTG-TAAAAATATCTTTGAGTTTGTTTCTTTGGAAACAAAATTGTCTCT
1 CTTGAGACAATTT-TTGAGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTGTCTCT
* * *
1761113 CTTGAGATAATTTCTTTTGAGAAAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAGTTTTGTCT
1 CTTGAGACAA--T-TTTTGAGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAA--ATTGTCT
1761178 CT
61 CT
1761180 CTTGAGACAGATTTTTGAGAAAAAAATCTTTGAGTTTGTTTCT
1 CTTGAGACA-ATTTTTGAGAAAAAAATCTTTGAGTTTGTTTCT
1761223 CTTAAAACAA
Statistics
Matches: 96, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
62 9 0.09
64 4 0.04
65 65 0.68
66 1 0.01
67 16 0.17
68 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (62 bp):
CTTGAGACAATTTTTGAGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTGTCTCT
Found at i:1761553 original size:42 final size:41
Alignment explanation
Indices: 1761457--1761563 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 41
1761447 AATGGCATGT
1761457 CGTTCTCATCGCGTAGGAACCGTGTCATCCTCCGACCAGAC
1 CGTTCTCATCGCGTAGGAACCGTGTCATCCTCCGACCAGAC
* * *
1761498 C-TCCTCATAGCGTAGGAGCCGTGTCA-CC-CCTGATAACCAG-C
1 CGTTCTCATCGCGTAGGAACCGTGTCATCCTCC-G---ACCAGAC
1761539 CGTTCTCATCGCGTAGGAACCGTGT
1 CGTTCTCATCGCGTAGGAACCGTGT
1761564 TATCACTCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
38 2 0.04
39 3 0.05
40 22 0.40
41 3 0.05
42 25 0.45
ACGTcount: A:0.20, C:0.35, G:0.23, T:0.22
Consensus pattern (41 bp):
CGTTCTCATCGCGTAGGAACCGTGTCATCCTCCGACCAGAC
Found at i:1761666 original size:134 final size:133
Alignment explanation
Indices: 1761400--1761851 Score: 438
Period size: 134 Copynumber: 3.4 Consensus size: 133
1761390 TTAACCCTAA
* * * * * * * * *
1761400 ATAACCAGCCATCCTCATCACGTAGAAACCGAGTTATTA-TC--GCTAATA-ATGGCATGTCGTT
1 ATAACCAGCCATTCTCATCGCGTAGGAACCGTGTTATCACTCTTCCTAA-AGATGGCCTGCCGTC
* *
1761461 CTCATCGCGTAGGAACCGTGTCATCCTCC-GACCAGACCTCCTCATAGCGTAGGAGCCGTGTCAC
65 CTCATCGCGTAGGAACCGTGTCATCCCCCTGACCAGACCTCCTCACA-CGTAGGAGCCGTGTCAC
* *
1761525 CCCTG
129 TCATG
*
1761530 ATAACCAGCCGTTCTCATCGCGTAGGAACCGTGTTATCACTCTTCCTAAAGATGGCCTGCCGTCC
1 ATAACCAGCCATTCTCATCGCGTAGGAACCGTGTTATCACTCTTCCTAAAGATGGCCTGCCGTCC
* ** * *
1761595 TCATCACGTAGGAATTGTGTCATCCCCCTGACCAGACCTCCTCACCACGTAGGAGTCATGTCACT
66 TCATCGCGTAGGAACCGTGTCATCCCCCTGACCAGACCTCCTCA-CACGTAGGAGCCGTGTCACT
1761660 CATG
130 CATG
* * * * * *
1761664 ATAACCAGCAATTTTCATCACGTAGGAACCGTGTTAT---TATTCCTAAAGATGGTCTGCTGTCC
1 ATAACCAGCCATTCTCATCGCGTAGGAACCGTGTTATCACTCTTCCTAAAGATGGCCTGCCGTCC
* * * *
1761726 TTATCGTGTAGGAACCATGTCAT-CCCCTGACCAGACCTCCTCATCACGTAGAAGCCGTGTCACT
66 TCATCGCGTAGGAACCGTGTCATCCCCCTGACCAGACCTCCTCA-CACGTAGGAGCCGTGTCACT
*
1761790 CTTAG
130 CAT-G
* * * * * * * *
1761795 ATAATCAACCATCCTCATTGCGAAGGAACCGTGTTGTCACCCTT-TTCAAAGATGGCC
1 ATAACCAGCCATTCTCATCGCGTAGGAACCGTGTTATCACTCTTCCT-AAAGATGGCC
1761852 AGAACTCTTC
Statistics
Matches: 261, Mismatches: 50, Indels: 18
0.79 0.15 0.05
Matches are distributed among these distances:
130 72 0.28
131 70 0.27
132 1 0.00
133 40 0.15
134 77 0.30
135 1 0.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (133 bp):
ATAACCAGCCATTCTCATCGCGTAGGAACCGTGTTATCACTCTTCCTAAAGATGGCCTGCCGTCC
TCATCGCGTAGGAACCGTGTCATCCCCCTGACCAGACCTCCTCACACGTAGGAGCCGTGTCACTC
ATG
Found at i:1761822 original size:131 final size:131
Alignment explanation
Indices: 1761400--1761829 Score: 458
Period size: 130 Copynumber: 3.3 Consensus size: 131
1761390 TTAACCCTAA
* * * * * * *
1761400 ATAACCAGCCATCCTCATCACGTAGAAACCGAGTTAT-TA-TCGCTAATA-ATGGCATGTCGTTC
1 ATAACCAGCCATTCTCATCGCGTAGGAACCGTGTTATCTATTC-CTAA-AGATGGCCTGCCGTCC
1761462 TCATCGCGTAGGAACCGTGTCATCCTCC-GACCAGACCTCCTCAT-AGCGTAGGAGCCGTGTCAC
64 TCATCGCGTAGGAACCGTGTCATCC-CCTGACCAGACCTCCTCATCA-CGTAGGAGCCGTGTCAC
* *
1761525 CCCTG
127 TCATG
* *
1761530 ATAACCAGCCGTTCTCATCGCGTAGGAACCGTGTTATCACTCTTCCTAAAGATGGCCTGCCGTCC
1 ATAACCAGCCATTCTCATCGCGTAGGAACCGTGTTAT--CTATTCCTAAAGATGGCCTGCCGTCC
* ** * * *
1761595 TCATCACGTAGGAATTGTGTCATCCCCCTGACCAGACCTCCTCACCACGTAGGAGTCATGTCACT
64 TCATCGCGTAGGAACCGTGTCAT-CCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACT
1761660 CATG
128 CATG
* * * * * *
1761664 ATAACCAGCAATTTTCATCACGTAGGAACCGTGTTAT-TATTCCTAAAGATGGTCTGCTGTCCTT
1 ATAACCAGCCATTCTCATCGCGTAGGAACCGTGTTATCTATTCCTAAAGATGGCCTGCCGTCCTC
* * * *
1761728 ATCGTGTAGGAACCATGTCATCCCCTGACCAGACCTCCTCATCACGTAGAAGCCGTGTCACTCTT
66 ATCGCGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACTCAT
1761793 AG
131 -G
* * * * *
1761795 ATAATCAACCATCCTCATTGCGAAGGAACCGTGTT
1 ATAACCAGCCATTCTCATCGCGTAGGAACCGTGTT
1761830 GTCACCCTTT
Statistics
Matches: 248, Mismatches: 43, Indels: 17
0.81 0.14 0.06
Matches are distributed among these distances:
130 71 0.29
131 67 0.27
132 1 0.00
133 38 0.15
134 70 0.28
135 1 0.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (131 bp):
ATAACCAGCCATTCTCATCGCGTAGGAACCGTGTTATCTATTCCTAAAGATGGCCTGCCGTCCTC
ATCGCGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACTCAT
G
Found at i:1761894 original size:264 final size:264
Alignment explanation
Indices: 1761400--1761918 Score: 590
Period size: 264 Copynumber: 2.0 Consensus size: 264
1761390 TTAACCCTAA
* *
1761400 ATAACCAGCCATCCTCATCACGTAGAAACCGAGTTATTATCGCTAATAATGGCATGTCGTTCTCA
1 ATAACCAGCAATCCTCATCACGTAGAAACCGAGTTATTATCGCTAATAATGGCATGTCGTCCTCA
* *
1761465 TCGCGTAGGAACCGTGTCATCCTCCGACCAGACCTCCTCATAGCGTAGGAGCCGTGTCACCCCTG
66 TCGCGTAGGAACCATGTCATCCTCCGACCAGACCTCCTCATAGCGTAGAAGCCGTGTCACCCCTG
* * * * * * *
1761530 ATAACCAGCCGTTCTCATCGCGTAGGAACCGTGTTATCACTCTTCCTAAAGATGGCCTGCCGTCC
131 ATAACCAACCATCCTCATCGCGAAGGAACCGTGTTATCACCCTTCCTAAAGATGGCCAGACGTCC
**
1761595 TCATCACGTAGGAATTGTGTCATCCCCCTGACCAGACCTCCTCACCACGTAGGAGTCATGTCACT
196 TCATCACGTAGGAACCGTGTCATCCCCCTGACCAGACCTCCTCACCACGTAGGAGTCATGTCACT
1761660 CATG
261 CATG
** * *
1761664 ATAACCAGCAATTTTCATCACGTAGGAACCGTGTTATTATTC-CTAA-AGATGGTC-TG-CTGTC
1 ATAACCAGCAATCCTCATCACGTAGAAACCGAGTTATTA-TCGCTAATA-ATGG-CATGTC-GTC
* *
1761725 CTTATCGTGTAGGAACCATGTCATCC-CCTGACCAGACCTCCTCATCA-CGTAGAAGCCGTGTCA
62 CTCATCGCGTAGGAACCATGTCATCCTCC-GACCAGACCTCCTCAT-AGCGTAGAAGCCGTGTCA
* * * * * *
1761788 CTCTTAGATAATCAACCATCCTCATTGCGAAGGAACCGTGTTGTCACCCTT-TTCAAAGATGGCC
125 CCCCT-GATAACCAACCATCCTCATCGCGAAGGAACCGTGTTATCACCCTTCCT-AAAGATGGCC
* * * ** * *
1761852 AGAAC-TCTTCATCACGTA-TAAGCCGTGTCATTCCCC-GACCAGATTTCCTTATCACGTAGGAG
188 AG-ACGTCCTCATCACGTAGGAA-CCGTGTCATCCCCCTGACCAGACCTCCTCACCACGTAGGAG
1761914 TCATG
251 TCATG
1761919 CCACCTTTAG
Statistics
Matches: 213, Mismatches: 32, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
263 4 0.02
264 133 0.62
265 75 0.35
266 1 0.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (264 bp):
ATAACCAGCAATCCTCATCACGTAGAAACCGAGTTATTATCGCTAATAATGGCATGTCGTCCTCA
TCGCGTAGGAACCATGTCATCCTCCGACCAGACCTCCTCATAGCGTAGAAGCCGTGTCACCCCTG
ATAACCAACCATCCTCATCGCGAAGGAACCGTGTTATCACCCTTCCTAAAGATGGCCAGACGTCC
TCATCACGTAGGAACCGTGTCATCCCCCTGACCAGACCTCCTCACCACGTAGGAGTCATGTCACT
CATG
Found at i:1762241 original size:3 final size:3
Alignment explanation
Indices: 1762221--1762262 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
1762211 TCTACAAAAA
1762221 TAT TAT T-T TAAT TA- TAT TAT TAT GTAT TAT TAT TAT TAT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
1762263 ATTTTTTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 4 0.11
3 26 0.74
4 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1764262 original size:16 final size:18
Alignment explanation
Indices: 1764241--1764278 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1764231 TTTCGAGTAT
1764241 TTTTTTA-TCAT-TTTTA
1 TTTTTTATTCATGTTTTA
*
1764257 TTTTTTATTCTTGTTTTA
1 TTTTTTATTCATGTTTTA
1764275 TTTT
1 TTTT
1764279 ATTTTTGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 3 0.16
18 9 0.47
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTTTATTCATGTTTTA
Found at i:1765688 original size:16 final size:17
Alignment explanation
Indices: 1765667--1765709 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
1765657 TCTCTTGTAA
1765667 GGATGAA-AACACTTTT
1 GGATGAATAACACTTTT
*
1765683 GGATGAATGTAACTCTTTT
1 GGATGAA--TAACACTTTT
1765702 GGATGAAT
1 GGATGAAT
1765710 GAAACTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 7 0.30
17 1 0.04
19 15 0.65
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.35
Consensus pattern (17 bp):
GGATGAATAACACTTTT
Found at i:1765702 original size:19 final size:19
Alignment explanation
Indices: 1765673--1765719 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
1765663 GTAAGGATGA
*
1765673 AAACACTTTTGGATGAATG
1 AAACTCTTTTGGATGAATG
*
1765692 TAACTCTTTTGGATGAATG
1 AAACTCTTTTGGATGAATG
1765711 AAACTCTTT
1 AAACTCTTT
1765720 CTAAGAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (19 bp):
AAACTCTTTTGGATGAATG
Found at i:1769381 original size:66 final size:59
Alignment explanation
Indices: 1769167--1769387 Score: 210
Period size: 65 Copynumber: 3.4 Consensus size: 59
1769157 TATCAGTATC
* **
1769167 CTTTTAGTTGTTTCTCTAT-AAACAAAATTTTGTCTCTCGAGACAGTTTCTTTAAAAAAAAGT
1 CTTTGAGTTGTTTC-CT-TGAAACAAAATTTTGTCTCTCGAGACAGTTT-TTTTGAAAAAA-T
* * *
1769229 CTTTGAGTCTGTTTCTCTGGAAACAAAATTTTGTCTCTATTGAGACAATTTCTTTTGAGAAAAAT
1 CTTTGAGT-TGTTTC-CTTGAAACAAAATTTTGTCTC--TCGAGACAGTTT-TTTTGA-AAAAAT
1769294 CTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAGTTTATTTTGAAAACACCTA
1 CTTTGAG-TTGTTTCC-TTGAAACAAAATTTTGTCTCTCGAGACAGTTT-TTTTGAAAA-A---A
1769359 T
59 T
1769360 CTTTGAGATTGTTTTCCTTGAAACAAAA
1 CTTTGAG-TTG-TTTCCTTGAAACAAAA
1769388 CAAACCCTCT
Statistics
Matches: 136, Mismatches: 11, Indels: 20
0.81 0.07 0.12
Matches are distributed among these distances:
62 10 0.07
63 43 0.32
64 1 0.01
65 48 0.35
66 29 0.21
67 5 0.04
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.42
Consensus pattern (59 bp):
CTTTGAGTTGTTTCCTTGAAACAAAATTTTGTCTCTCGAGACAGTTTTTTTGAAAAAAT
Found at i:1774240 original size:136 final size:131
Alignment explanation
Indices: 1773983--1774465 Score: 501
Period size: 133 Copynumber: 3.6 Consensus size: 131
1773973 ACCATTATCC
* * *
1773983 CTAATGATGGCATGT-GATCCTCATCACGTAGGAACCGTGCCATCCCCCGACCAGACCTCCTCGT
1 CTAAAGATGGCATGTCG-TCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCAT
* *
1774047 CACGTAGGAGCCGTGTCATCCCTGATAACCAACCGTCCTCATCGCATAGGAATCGTGTTATCACC
65 CACGTAGGAGCCGTGTCA-CCCTGATAACCAACCGTCCTCATCGCGTAGGAACCGTGTTATCACC
1774112 CTTT
129 C-TT
** *
1774116 CTAAAGATGGCATGTCGTCCTCATCACGTAAAAAACCATGTCATTCCCCCCGACCAGACCTCCTC
1 CTAAAGATGGCATGTCGTCCTCATCACGT-AGGAACCGTGTCA-T-CCCCCGACCAGACCTCCTC
* * * *
1774181 ATCACGTAGGAGCCATGTCACCCATGATAACCAGCCGTCCTCATCACGTAAGAACCGTGTTATCA
63 ATCACGTAGGAGCCGTGTCACCC-TGATAACCAACCGTCCTCATCGCGTAGGAACCGTGTTATCA
*
1774246 TCC--
127 CCCTT
* ** * * * * *
1774249 CTAAAGATGGCCTACCATCTTCATCACGTAGGAACTGTGTCAT-CCCTGACCATACCTCCTCATC
1 CTAAAGATGGCATGTCGTCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCATC
** * *
1774313 ACGTACAAGCCGTGTCACCCTTAGATAACCAACCGTACTCATCGCGTAGGAACCGTGTTATTACC
66 ACGTAGGAGCCGTGTCACCC-T-GATAACCAACCGTCCTCATCGCGTAGGAACCGTGTTATCACC
1774378 CTT
129 CTT
* * * ** * **
1774381 CCTAAAGATGGCCA-GAAC-TCTTCATCACGTATGAGTCGTGTCATCCACCGACCAGATTTCCTC
1 -CTAAAGATGG-CATG-TCGTCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTC
**
1774444 ATCACGTAGGAGTTGTGTCACC
63 ATCACGTAGGAGCCGTGTCACC
1774466 TTTAGATGAC
Statistics
Matches: 288, Mismatches: 50, Indels: 23
0.80 0.14 0.06
Matches are distributed among these distances:
129 37 0.13
130 37 0.13
131 1 0.00
132 9 0.03
133 82 0.28
134 43 0.15
135 4 0.01
136 75 0.26
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (131 bp):
CTAAAGATGGCATGTCGTCCTCATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCATC
ACGTAGGAGCCGTGTCACCCTGATAACCAACCGTCCTCATCGCGTAGGAACCGTGTTATCACCCT
T
Found at i:1774674 original size:3 final size:3
Alignment explanation
Indices: 1774666--1774724 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
1774656 ATACCAAAAA
* * *
1774666 TAT TAT TA- TAT TAT AAA TAT TGAT TA- TAT TAT TAT TAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
1774710 TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT T
1774725 TACATGTGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 6 0.13
3 37 0.80
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1775697 original size:15 final size:16
Alignment explanation
Indices: 1775677--1775716 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
1775667 TAAGAGCTAA
1775677 TAGCATGTTTGGT-CC
1 TAGCATGTTTGGTCCC
1775692 TAGCATGTTTGGTCCC
1 TAGCATGTTTGGTCCC
1775708 T-GCATGTTT
1 TAGCATGTTT
1775717 AACCTTACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 21 0.88
16 3 0.12
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.42
Consensus pattern (16 bp):
TAGCATGTTTGGTCCC
Found at i:1776211 original size:30 final size:30
Alignment explanation
Indices: 1776171--1776313 Score: 164
Period size: 30 Copynumber: 4.8 Consensus size: 30
1776161 GCCCTTCAAT
* * * *
1776171 TTTTTTCTATTTAAGTTCTTTAACTTTATG
1 TTTTTACTATTTTAGTCCTTTAACTTTTTG
*
1776201 TTTTTACTATTTTAGTCCTTTAACTTTCT-
1 TTTTTACTATTTTAGTCCTTTAACTTTTTG
*
1776230 ATTTTAGCTATTTTAGTCCTTTAACTTTTTG
1 TTTTTA-CTATTTTAGTCCTTTAACTTTTTG
* *
1776261 -TTTTAGCTATTTTAGTCCCTTAAGTTTTTG
1 TTTTTA-CTATTTTAGTCCTTTAACTTTTTG
**
1776291 TTTTTGTTATTTTAGTCCTTTAA
1 TTTTTACTATTTTAGTCCTTTAA
1776314 ATGTCTATTT
Statistics
Matches: 99, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
29 5 0.05
30 90 0.91
31 4 0.04
ACGTcount: A:0.18, C:0.13, G:0.08, T:0.61
Consensus pattern (30 bp):
TTTTTACTATTTTAGTCCTTTAACTTTTTG
Found at i:1776325 original size:30 final size:30
Alignment explanation
Indices: 1776202--1776402 Score: 144
Period size: 30 Copynumber: 6.8 Consensus size: 30
1776192 AACTTTATGT
*
1776202 TTTTA-CTATTTTAGTCCTTTAACTTTCTA
1 TTTTAGCTATTTTAGTCCTTTAAATTTCTA
* * *
1776231 TTTTAGCTATTTTAGTCCTTTAACTTTTTG
1 TTTTAGCTATTTTAGTCCTTTAAATTTCTA
* * * *
1776261 TTTTAGCTATTTTAGTCCCTTAAGTTTTTG
1 TTTTAGCTATTTTAGTCCTTTAAATTTCTA
* * *
1776291 TTTTTGTTATTTTAGTCCTTTAAATGTCTA
1 TTTTAGCTATTTTAGTCCTTTAAATTTCTA
** * *
1776321 TTTT-TTTAATTTTTTGTCCTTTAAATATCTA
1 TTTTAGCT-A-TTTTAGTCCTTTAAATTTCTA
* **
1776352 TATTTA-CTA-TTTAGACCTTTATGTTTC-A
1 T-TTTAGCTATTTTAGTCCTTTAAATTTCTA
* *
1776380 TTTTTA-CTGTTTTAGCCCTTTAA
1 -TTTTAGCTATTTTAGTCCTTTAA
1776403 GTTTATGGTT
Statistics
Matches: 142, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
28 7 0.05
29 32 0.23
30 78 0.55
31 21 0.15
32 4 0.03
ACGTcount: A:0.20, C:0.13, G:0.08, T:0.59
Consensus pattern (30 bp):
TTTTAGCTATTTTAGTCCTTTAAATTTCTA
Found at i:1776466 original size:2 final size:2
Alignment explanation
Indices: 1776459--1776493 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1776449 CCTTATTTTG
1776459 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 T
1776494 TTCATTTTGT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1780164 original size:20 final size:20
Alignment explanation
Indices: 1780139--1780176 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1780129 TGTTTTGACC
1780139 AGAAGTTTCGAAACTTTCAA
1 AGAAGTTTCGAAACTTTCAA
*
1780159 AGAAGTTTTGAAACTTTC
1 AGAAGTTTCGAAACTTTC
1780177 TAAAACATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (20 bp):
AGAAGTTTCGAAACTTTCAA
Found at i:1780245 original size:20 final size:20
Alignment explanation
Indices: 1780195--1780247 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
1780185 AAGACTTTTG
* *
1780195 AGTTTCAAAAC-TTCACAAG
1 AGTTTCGAAACTTTCACAAA
* * *
1780214 AGTTTTGTAACTTTCATAAA
1 AGTTTCGAAACTTTCACAAA
1780234 AGTTTCGAAACTTT
1 AGTTTCGAAACTTT
1780248 ACTTGAAGTT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (20 bp):
AGTTTCGAAACTTTCACAAA
Found at i:1783670 original size:18 final size:17
Alignment explanation
Indices: 1783646--1783691 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
1783636 TGTTTATGAG
1783646 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
* *
1783664 TGAATTGGAATCTGTTA
1 GGAATTGGAATCTGTAA
1783681 GGAATTGGAAT
1 GGAATTGGAAT
1783692 TCAATTCCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:1787994 original size:20 final size:20
Alignment explanation
Indices: 1787969--1788008 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1787959 TTGTATTATC
*
1787969 TTATAAAATTAATAAATTTT
1 TTATAAAATAAATAAATTTT
* *
1787989 TTATAACATAAATGAATTTT
1 TTATAAAATAAATAAATTTT
1788009 ATTTCTATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
TTATAAAATAAATAAATTTT
Found at i:1793750 original size:27 final size:26
Alignment explanation
Indices: 1793716--1793786 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 26
1793706 TTAAATTTAT
1793716 AATATTTTATATATATTAACTTTAAG-A
1 AATATTTT-TATATATTAACTTT-AGTA
1793743 AATA-TTTT-TATATTAA-TTTAGTA
1 AATATTTTTATATATTAACTTTAGTA
1793766 AATATATTTTAT-TATTAACTT
1 AATAT-TTTTATATATTAACTT
1793787 AATTTAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
22 2 0.05
23 8 0.21
24 8 0.21
25 11 0.28
26 6 0.15
27 4 0.10
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (26 bp):
AATATTTTTATATATTAACTTTAGTA
Found at i:1793758 original size:24 final size:25
Alignment explanation
Indices: 1793727--1793786 Score: 81
Period size: 24 Copynumber: 2.4 Consensus size: 25
1793717 ATATTTTATA
1793727 TATATTAACTTTAAG-AAATAT-TTT
1 TATATTAACTTT-AGTAAATATATTT
1793751 TATATTAA-TTTAGTAAATATATTT
1 TATATTAACTTTAGTAAATATATTT
1793775 TATTATTAACTT
1 TA-TATTAACTT
1793787 AATTTAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
22 2 0.06
23 9 0.28
24 13 0.41
25 6 0.19
26 2 0.06
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (25 bp):
TATATTAACTTTAGTAAATATATTT
Found at i:1793781 original size:25 final size:24
Alignment explanation
Indices: 1793709--1793783 Score: 77
Period size: 24 Copynumber: 3.1 Consensus size: 24
1793699 ACATAACTTA
1793709 AATTTA-T-AATATTTTATATATATT
1 AATTTAGTAAATATTTT-TAT-TATT
1793733 AACTTTAAG-AAATATTTTTA-TATT
1 AA-TTT-AGTAAATATTTTTATTATT
1793757 AATTTAGTAAATATATTTTATTATT
1 AATTTAGTAAATAT-TTTTATTATT
1793782 AA
1 AA
1793784 CTTAATTTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
22 2 0.05
23 9 0.20
24 13 0.30
25 9 0.20
26 3 0.07
27 8 0.18
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (24 bp):
AATTTAGTAAATATTTTTATTATT
Found at i:1793794 original size:27 final size:28
Alignment explanation
Indices: 1793702--1793829 Score: 78
Period size: 27 Copynumber: 4.8 Consensus size: 28
1793692 TATAAATACA
*
1793702 TAACTTAAATTTATA-ATATTTTATATA-
1 TAACTT-AATTTAAATATATTTTATATAT
*
1793729 T-A-TTAACTTTAAGAAATATTTT-TATAT
1 TAACTTAA-TTTAA-ATATATTTTATATAT
* *
1793756 TAA-TTTA-GTAAATATATTTTAT-TAT
1 TAACTTAATTTAAATATATTTTATATAT
*
1793781 TAACTTAATTTAAA-ATTATTTTATCT-T
1 TAACTTAATTTAAATA-TATTTTATATAT
** *
1793808 TATTTTAATTTAAAAATATTTT
1 TAACTTAATTTAAATATATTTT
1793830 TTTGTGAAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
24 2 0.02
25 20 0.24
26 14 0.17
27 40 0.49
28 6 0.07
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (28 bp):
TAACTTAATTTAAATATATTTTATATAT
Found at i:1797547 original size:21 final size:21
Alignment explanation
Indices: 1797479--1797555 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
1797469 TTGATGCATG
* *
1797479 GGGTATCGATACCTGTATGAA
1 GGGTATCGATACCTATATGGA
**
1797500 AAGTATCGATACC-ATATGGA
1 GGGTATCGATACCTATATGGA
*
1797520 GGAGGTATCGATACCTATGTGGA
1 -G-GGTATCGATACCTATATGGA
1797543 GGGTATCGATACC
1 GGGTATCGATACC
1797556 CAGGGAGCTT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 5 0.11
21 23 0.50
22 12 0.26
23 6 0.13
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.26
Consensus pattern (21 bp):
GGGTATCGATACCTATATGGA
Found at i:1798572 original size:28 final size:28
Alignment explanation
Indices: 1798526--1798602 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
1798516 TCGAGGGTTC
*
1798526 TATGTGGTCC-TTCGAGACATATGTATTA
1 TATGTGGTCCTTTAG-GACATATGTATTA
*
1798554 TATGTGGTCCTTTAGGACATATGTGTTA
1 TATGTGGTCCTTTAGGACATATGTATTA
*
1798582 TATGTGGTCCTTTGGGACATA
1 TATGTGGTCCTTTAGGACATA
1798603 GTGGTCATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 42 0.93
29 3 0.07
ACGTcount: A:0.22, C:0.13, G:0.25, T:0.40
Consensus pattern (28 bp):
TATGTGGTCCTTTAGGACATATGTATTA
Found at i:1798902 original size:22 final size:25
Alignment explanation
Indices: 1798855--1798905 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 25
1798845 AAATAAGTAC
1798855 ATATGTGTATGTGTTATATGAGATG
1 ATATGTGTATGTGTTATATGAGATG
*
1798880 ATATGTGT-T-TGTT-TATGATATG
1 ATATGTGTATGTGTTATATGAGATG
1798902 ATAT
1 ATAT
1798906 TAGTAATGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 12 0.48
23 4 0.16
24 1 0.04
25 8 0.32
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (25 bp):
ATATGTGTATGTGTTATATGAGATG
Found at i:1799043 original size:20 final size:20
Alignment explanation
Indices: 1799015--1799063 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1799005 GTAATGATAA
*
1799015 GTATGTAGATAATGATTTAT
1 GTATGTAGATAATAATTTAT
* *
1799035 GTATATAGATGATAATTTAT
1 GTATGTAGATAATAATTTAT
1799055 GTATGTAGA
1 GTATGTAGA
1799064 CAAGTATTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (20 bp):
GTATGTAGATAATAATTTAT
Found at i:1801882 original size:22 final size:21
Alignment explanation
Indices: 1801854--1801905 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
1801844 GTATGAACAA
1801854 TATCGATATCATATGAAGGA-GG
1 TATCGATA-CATATG-AGGAGGG
* *
1801876 TATCGATACCTATGTGGAGGG
1 TATCGATACATATGAGGAGGG
1801897 TATCGATAC
1 TATCGATAC
1801906 CCGGGAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 3 0.11
21 16 0.59
22 8 0.30
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (21 bp):
TATCGATACATATGAGGAGGG
Found at i:1801953 original size:19 final size:20
Alignment explanation
Indices: 1801929--1801981 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
1801919 AGCTAATTTT
1801929 GGTATCGGTACCT-GAGTAG-
1 GGTATCGGTACCTAGA-TAGA
*
1801948 GGTATCAGTACCCTAGCATAGA
1 GGTATCGGTA-CCTAG-ATAGA
1801970 GGTATCGGTACC
1 GGTATCGGTACC
1801982 CTAAGGGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 9 0.32
20 3 0.11
21 6 0.21
22 10 0.36
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.25
Consensus pattern (20 bp):
GGTATCGGTACCTAGATAGA
Found at i:1806329 original size:41 final size:41
Alignment explanation
Indices: 1806225--1806443 Score: 242
Period size: 41 Copynumber: 5.3 Consensus size: 41
1806215 CTGTAAACAC
* * *
1806225 AAATGCCACTAAAGTATGAGTCTATAGCGACATTTGTATAAA
1 AAATGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTAT-AA
* * *
1806267 AAATTCCACTAAAGCATGAGTCTATAGCGGCGTTTGTATAA
1 AAATGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAA
* * * * *
1806308 AAACGCCACTAAAGTACGAGTCTTTGGTGGCATTTGTATAA
1 AAATGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAA
* * * *
1806349 AAGTGCCACTAAAGTACGATTCTTTAGCGGCGTTTGT-CAA
1 AAATGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAA
* * *
1806389 AAATGCCACTAAAGTATGAGTATTTAGCAGCGTTTGTTCTAA
1 AAATGCCACTAAAGTATGAGTCTTTAGCGGCGTTTG-TATAA
*
1806431 AAATGCCGCTAAA
1 AAATGCCACTAAA
1806444 AATATCGTTA
Statistics
Matches: 149, Mismatches: 26, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
40 33 0.22
41 67 0.45
42 49 0.33
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (41 bp):
AAATGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAA
Done.