Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008027.1 Hibiscus syriacus cultivar Beakdansim tig00110503_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: 7662336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 38
Found at i:1738355 original size:28 final size:29
Alignment explanation
Indices: 1738043--1738356 Score: 235
Period size: 28 Copynumber: 10.9 Consensus size: 29
1738033 ACTTAAACTT
*
1738043 TTTTTAAAAACTATATTATATATAA-TAG
1 TTTTCAAAAACTATATTATATATAATTAG
*
1738071 TTTTC-AAAACCATATTATATGATAATTA-
1 TTTTCAAAAACTATATTATAT-ATAATTAG
*
1738099 TTTTCAAAAACTATACTATATATATAGTAATAG
1 TTTTCAAAAACTATA-T-TATATATA--ATTAG
* * * *
1738132 CTTTC-AAAACTACATTATATAATAACTAT
1 TTTTCAAAAACTATATTATAT-ATAATTAG
*
1738161 TTTTCAAAAACTATATTATGTATAA-TAG
1 TTTTCAAAAACTATATTATATATAATTAG
* * * *
1738189 TTTTCAAAATC-AAATTGTATAATAACTA-
1 TTTTCAAAAACTATATTATAT-ATAATTAG
* *
1738217 TTTT-AACAAACTATACTATATTTATAA-TAA
1 TTTTCAA-AAACTATA-T-TATATATAATTAG
1738247 TTTTC--AAACTTATATTATATAATAATTA-
1 TTTTCAAAAAC-TATATTATAT-ATAATTAG
* *
1738275 TTTTCAAAAATTATACTATATATAA-TAG
1 TTTTCAAAAACTATATTATATATAATTAG
*
1738303 TTTTC-AAAACTATGTTATATAATAATTA-
1 TTTTCAAAAACTATATTATAT-ATAATTAG
**
1738331 TTTTCAAAAACTATGCTATATATAAT
1 TTTTCAAAAACTATATTATATATAAT
1738357 ATACATATGC
Statistics
Matches: 232, Mismatches: 27, Indels: 54
0.74 0.09 0.17
Matches are distributed among these distances:
27 40 0.17
28 73 0.31
29 58 0.25
30 34 0.15
31 12 0.05
32 11 0.05
33 4 0.02
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (29 bp):
TTTTCAAAAACTATATTATATATAATTAG
Found at i:1745796 original size:39 final size:38
Alignment explanation
Indices: 1745716--1745822 Score: 112
Period size: 39 Copynumber: 2.9 Consensus size: 38
1745706 AAAATCAGAT
* *
1745716 TTTC-ATAT-AAAAATCAGATTGCAACCTAAAATCTGA
1 TTTCTATATGAAAAATCAGGTTGCAACCTAAAATATGA
* * *
1745752 TTTCTATATGAAATATCAGGTTGCAACATTAAAATATGG
1 TTTCTATATGAAAAATCAGGTTGCAAC-CTAAAATATGA
* * *
1745791 TTTCTAAATGAAAAATCAAGTTGCGACC-AAAA
1 TTTCTATATGAAAAATCAGGTTGCAACCTAAAA
1745823 GTTTGGTTCC
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
36 4 0.07
37 8 0.14
38 15 0.26
39 31 0.53
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (38 bp):
TTTCTATATGAAAAATCAGGTTGCAACCTAAAATATGA
Found at i:1749196 original size:2 final size:2
Alignment explanation
Indices: 1749184--1749232 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
1749174 CTATTAGCCA
1749184 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1749227 AT AT AT
1 AT AT AT
1749233 TTTAAGAACT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1750511 original size:24 final size:24
Alignment explanation
Indices: 1750484--1750552 Score: 102
Period size: 24 Copynumber: 2.9 Consensus size: 24
1750474 CATATATCAT
* *
1750484 AACAGAATCTAGGTCAGGTATTAG
1 AACAGAATCCATGTCAGGTATTAG
*
1750508 AACAGAATCCATGTCAAGTATTAG
1 AACAGAATCCATGTCAGGTATTAG
*
1750532 AATAGAATCCATGTCAGGTAT
1 AACAGAATCCATGTCAGGTAT
1750553 CATAAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.26
Consensus pattern (24 bp):
AACAGAATCCATGTCAGGTATTAG
Found at i:1754409 original size:24 final size:24
Alignment explanation
Indices: 1754353--1754416 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
1754343 ATCATAACAA
* * *
1754353 AATCCAGGCCAGGTATTAGAATAT
1 AATCCATGTCAGGTATTAGAATAG
1754377 AATCCATGTCAGGTATTAGAATAG
1 AATCCATGTCAGGTATTAGAATAG
* *
1754401 AATCTATGTCATGTAT
1 AATCCATGTCAGGTAT
1754417 CATAACAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (24 bp):
AATCCATGTCAGGTATTAGAATAG
Found at i:1756814 original size:22 final size:22
Alignment explanation
Indices: 1756771--1756814 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1756761 GCTTGGTTCA
* * *
1756771 CAATTTTGAACGGTGAAGAACT
1 CAATTTTGAAAGGTCAAAAACT
*
1756793 CAATTTTGAAATGTCAAAAACT
1 CAATTTTGAAAGGTCAAAAACT
1756815 TTGACTTCCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (22 bp):
CAATTTTGAAAGGTCAAAAACT
Found at i:1758273 original size:24 final size:24
Alignment explanation
Indices: 1758246--1758295 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1758236 GATCATAATC
* *
1758246 CATGTCACGTATTAGAATAGAATT
1 CATGTCACGTATCAGAACAGAATT
* *
1758270 CATGTCAGGTATCATAACAGAATT
1 CATGTCACGTATCAGAACAGAATT
1758294 CA
1 CA
1758296 AATCGGAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (24 bp):
CATGTCACGTATCAGAACAGAATT
Found at i:1762085 original size:24 final size:24
Alignment explanation
Indices: 1762053--1762161 Score: 110
Period size: 24 Copynumber: 4.5 Consensus size: 24
1762043 ATATATCAAA
* * * *
1762053 ATCAAAACATAATTCAGGTCAGAT
1 ATCAGAACAGAATCCAGGTCAGGT
*
1762077 ATCATAACAGAATCCAGGTCAGGT
1 ATCAGAACAGAATCCAGGTCAGGT
* * *
1762101 ATTAGAACATAATCCATGTCAGGT
1 ATCAGAACAGAATCCAGGTCAGGT
* * *
1762125 ATTAGAATAGAATCCATGTCAGGT
1 ATCAGAACAGAATCCAGGTCAGGT
*
1762149 ATCATAACAGAAT
1 ATCAGAACAGAAT
1762162 TCAAATTAGA
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26
Consensus pattern (24 bp):
ATCAGAACAGAATCCAGGTCAGGT
Found at i:1762137 original size:48 final size:48
Alignment explanation
Indices: 1762058--1762150 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
1762048 TCAAAATCAA
* *
1762058 AACATAATTCAGGTCAGATATCATAACAGAATCCAGGTCAGGTATTAG
1 AACATAATCCAGGTCAGATATCAGAACAGAATCCAGGTCAGGTATTAG
* * * * *
1762106 AACATAATCCATGTCAGGTATTAGAATAGAATCCATGTCAGGTAT
1 AACATAATCCAGGTCAGATATCAGAACAGAATCCAGGTCAGGTAT
1762151 CATAACAGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (48 bp):
AACATAATCCAGGTCAGATATCAGAACAGAATCCAGGTCAGGTATTAG
Found at i:1763899 original size:14 final size:14
Alignment explanation
Indices: 1763882--1763916 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
1763872 CATAAACAAA
1763882 CAAGCATA-ATAGTC
1 CAAGCATATATA-TC
1763896 CAAGCATATATATC
1 CAAGCATATATATC
1763910 CAAGCAT
1 CAAGCAT
1763917 TTTCCATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23
Consensus pattern (14 bp):
CAAGCATATATATC
Found at i:1764257 original size:7 final size:7
Alignment explanation
Indices: 1764245--1764298 Score: 81
Period size: 7 Copynumber: 7.4 Consensus size: 7
1764235 GTCAATGGTC
1764245 CGGTCAA
1 CGGTCAA
1764252 CGGTCAA
1 CGGTCAA
1764259 CGAGGTCAA
1 C--GGTCAA
*
1764268 CAGTCAA
1 CGGTCAA
1764275 CGGTCAA
1 CGGTCAA
1764282 CGGTCAA
1 CGGTCAA
1764289 CGGTCAA
1 CGGTCAA
1764296 CGG
1 CGG
1764299 GTAATCGGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
7 36 0.84
9 7 0.16
ACGTcount: A:0.30, C:0.28, G:0.30, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:1765607 original size:47 final size:47
Alignment explanation
Indices: 1765533--1765627 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
1765523 CAATTACAGG
1765533 TCAAATTCATAAAATGTCAAGTTAATAACAGATCGAGTAATACCAGT
1 TCAAATTCATAAAATGTCAAGTTAATAACAGATCGAGTAATACCAGT
* *
1765580 TCAAGTTCATAAAATGTCAAGTTAATAACAGATCGAGTAATACTAGT
1 TCAAATTCATAAAATGTCAAGTTAATAACAGATCGAGTAATACCAGT
1765627 T
1 T
1765628 GTTTACTAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (47 bp):
TCAAATTCATAAAATGTCAAGTTAATAACAGATCGAGTAATACCAGT
Found at i:1766982 original size:17 final size:17
Alignment explanation
Indices: 1766962--1766994 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1766952 AATTTCAATA
1766962 AAAATATGA-AAAAATTT
1 AAAATAT-ATAAAAATTT
1766979 AAAATATATAAAAATT
1 AAAATATATAAAAATT
1766995 CAAATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
AAAATATATAAAAATTT
Found at i:1769724 original size:28 final size:30
Alignment explanation
Indices: 1769689--1769751 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
1769679 TATATGAAAT
1769689 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATATTA
1769717 TATTAGTTTGTTAGTTTAAGTTATATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATATTA
1769747 TATTA
1 TATTA
1769752 TATAAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 20 0.61
29 1 0.03
30 12 0.36
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (30 bp):
TATTAGTTTGTTAGTTTAAGTTATATATTA
Found at i:1770251 original size:23 final size:24
Alignment explanation
Indices: 1770207--1770251 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1770197 TATTGTGTTT
**
1770207 AAAAATATTTAGTGTTGTTTTAAA
1 AAAAATATTTAGTGTTAATTTAAA
*
1770231 AAAAATATTTTGT-TTAATTTA
1 AAAAATATTTAGTGTTAATTTA
1770252 TATTGTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 6 0.33
24 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (24 bp):
AAAAATATTTAGTGTTAATTTAAA
Found at i:1777683 original size:20 final size:21
Alignment explanation
Indices: 1777647--1777703 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
1777637 TTTTGGTACA
*
1777647 GAGGGAA-TCGATACCCCC-AT
1 GAGGGAACT-GATTCCCCCTAT
*
1777667 GAGGGAACTGATTCCCCCTTT
1 GAGGGAACTGATTCCCCCTAT
1777688 GAAGGGGAACTGATTC
1 G-A-GGGAACTGATTC
1777704 AGGGGAATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 15 0.48
21 3 0.10
22 1 0.03
23 12 0.39
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (21 bp):
GAGGGAACTGATTCCCCCTAT
Found at i:1783144 original size:49 final size:49
Alignment explanation
Indices: 1783091--1783376 Score: 527
Period size: 49 Copynumber: 5.8 Consensus size: 49
1783081 GGCACCCATC
1783091 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1783140 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
* *
1783189 TATTATTAATATTTAATGATTTGATAATAATGATTAGTAATAATAAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
*
1783238 TATTATTAATATTTAATGATTTGATAGTAATGATTAATAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1783287 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
* *
1783336 TATTATTAATATTTAATTATTTGATAGTAATGAATAGTAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAAT
1783377 TATTAATAAT
Statistics
Matches: 229, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 229 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (49 bp):
TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
Found at i:1783400 original size:17 final size:18
Alignment explanation
Indices: 1783319--1783408 Score: 67
Period size: 17 Copynumber: 4.8 Consensus size: 18
1783309 GATAGTAATG
*
1783319 ATTAGTAATAATGAAATT
1 ATTAATAATAATGAAATT
* **
1783337 ATTATTAAT-ATTTAATT
1 ATTAATAATAATGAAATT
*
1783354 ATTTGATAGTAATGAATAGTAATT
1 A-TT-A-A-TAAT-AAT-GAAATT
1783378 ATTAATAATAATGAAATT
1 ATTAATAATAATGAAATT
1783396 A-TAATAATAATGA
1 ATTAATAATAATGA
1783409 TTTACTAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
17 19 0.32
18 16 0.27
19 4 0.07
20 4 0.07
21 5 0.08
22 1 0.02
23 4 0.07
24 6 0.10
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (18 bp):
ATTAATAATAATGAAATT
Found at i:1783449 original size:147 final size:146
Alignment explanation
Indices: 1783098--1783409 Score: 403
Period size: 147 Copynumber: 2.1 Consensus size: 146
1783088 ATCTATTATT
* * * * * *
1783098 AATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTG
1 AATATTTAATAATATGATACTAATGAGTAATAATAAT-AAATTATTATTAACATTTAATGATTTG
*
1783163 ATAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAATAATGATTAGTA
65 ATAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAATAATGAATAGTA
* * *
1783228 ATAATAAAATTATTATT
130 ATAATAAAATAATAATG
* * * * *
1783245 AATATTTAATGATTTGATAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTG
1 AATATTTAATAATATGATACTAATGAGTAATAATAAT-AAATTATTATTAACATTTAATGATTTG
* *
1783310 ATAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATTATTTGATAGTAATGAATAGTA
65 ATAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAATAATGAATAGTA
* *
1783375 ATTAT-TAATAATAATG
130 ATAATAAAATAATAATG
1783391 AA-ATTATAATAATAATGAT
1 AATATT-TAATAAT-ATGAT
1783410 TTACTAATAG
Statistics
Matches: 152, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
145 3 0.02
146 15 0.10
147 134 0.88
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.44
Consensus pattern (146 bp):
AATATTTAATAATATGATACTAATGAGTAATAATAATAAATTATTATTAACATTTAATGATTTGA
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAATAATGAATAGTAA
TAATAAAATAATAATG
Found at i:1783608 original size:12 final size:12
Alignment explanation
Indices: 1783587--1783641 Score: 69
Period size: 12 Copynumber: 4.7 Consensus size: 12
1783577 CATAAAAATG
1783587 ATTTAATAAT-A
1 ATTTAATAATAA
*
1783598 ATTTAAATAAT-G
1 ATTT-AATAATAA
*
1783610 ATTTAATAATGA
1 ATTTAATAATAA
1783622 ATTTAATAATAA
1 ATTTAATAATAA
1783634 ATTTAATA
1 ATTTAATA
1783642 TTTAATGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
11 10 0.26
12 29 0.74
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (12 bp):
ATTTAATAATAA
Found at i:1783609 original size:23 final size:24
Alignment explanation
Indices: 1783579--1783942 Score: 96
Period size: 26 Copynumber: 14.7 Consensus size: 24
1783569 CAATTAACCA
1783579 TAAA-AATGATTTAATAAT-AATT
1 TAAATAATGATTTAATAATGAATT
1783601 TAAATAATGATTTAATAATGAATT
1 TAAATAATGATTTAATAATGAATT
* * *
1783625 T-AATAATAAATTTAATATTTAA-T
1 TAAATAAT-GATTTAATAATGAATT
* ** * *
1783648 GATTTGATGATTTAGTAATG-ATT
1 TAAATAATGATTTAATAATGAATT
* * *
1783671 TGATAAAAATCATTATAGTAATG-ATT
1 T-A-AATAATGATT-TAATAATGAATT
*
1783697 CGATAATAATAATCATTATAATAATG-ATT
1 ---T-A-AATAATGATT-TAATAATGAATT
*
1783726 TAGTAATAATCATTATAATAATG-ATT
1 TA--AATAATGATT-TAATAATGAATT
* *
1783752 T-AATAATGATTTAAATATTTAA-T
1 TAAATAATGATTT-AATAATGAATT
* ** * *
1783775 GATTTGATGATTTAGTAATG-ATT
1 TAAATAATGATTTAATAATGAATT
*
1783798 TGATAATAATCATTATAATAATG-ATT
1 T-A-AATAATGATT-TAATAATGAATT
*
1783824 TAGTAATAATCATTATAATAATG-ATT
1 TA--AATAATGATT-TAATAATGAATT
1783850 TAATAATAATGA--TAATAATG-ATT
1 T-A-AATAATGATTTAATAATGAATT
* *
1783873 TAATAATAATAATGATAATAATG-ATT
1 T-A-AATAATGAT-TTAATAATGAATT
* * * *
1783899 TAATAGTAATTATTTAGTAATTATTT
1 TAA-A-TAATGATTTAATAATGAATT
*
1783925 TATAATAATAATTTAATA
1 TA-AATAATGATTTAATA
1783943 TTAATGATTT
Statistics
Matches: 269, Mismatches: 45, Indels: 53
0.73 0.12 0.14
Matches are distributed among these distances:
22 7 0.03
23 72 0.27
24 31 0.12
25 32 0.12
26 102 0.38
27 2 0.01
29 23 0.09
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (24 bp):
TAAATAATGATTTAATAATGAATT
Found at i:1783689 original size:26 final size:26
Alignment explanation
Indices: 1783663--1783958 Score: 256
Period size: 26 Copynumber: 11.6 Consensus size: 26
1783653 GATGATTTAG
* * *
1783663 TAATGATTTGATAAAAATCATTATAG
1 TAATGATTTAATAATAATCATTATAA
1783689 TAATGATTCGATAATAATAATCATTATAA
1 TAATGATT---TAATAATAATCATTATAA
*
1783718 TAATGATTTAGTAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
*
1783744 TAATGA-TT--TAATAATGATT-T-A
1 TAATGATTTAATAATAATCATTATAA
* * * *
1783765 -AAT-ATTTAATGATTTGATGATT-TAG
1 TAATGATTTAAT-A-ATAATCATTATAA
*
1783790 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
*
1783816 TAATGATTTAGTAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
*
1783842 TAATGATTTAATAAT-A--ATGATAA
1 TAATGATTTAATAATAATCATTATAA
* *
1783865 TAATGATTTAATAATAATAATGATAA
1 TAATGATTTAATAATAATCATTATAA
* * *
1783891 TAATGATTTAATAGTAATTATT-TAG
1 TAATGATTTAATAATAATCATTATAA
* * * *
1783916 TAATTATTTTATAATAATAATTTAATAT
1 TAATGATTTAATAATAATCA-TT-ATAA
1783944 TAATGATTTAATAAT
1 TAATGATTTAATAAT
1783959 TATTACTAAT
Statistics
Matches: 224, Mismatches: 28, Indels: 34
0.78 0.10 0.12
Matches are distributed among these distances:
19 1 0.00
20 5 0.02
21 1 0.00
22 2 0.01
23 32 0.14
24 9 0.04
25 27 0.12
26 103 0.46
27 6 0.03
28 15 0.07
29 23 0.10
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (26 bp):
TAATGATTTAATAATAATCATTATAA
Found at i:1783769 original size:127 final size:123
Alignment explanation
Indices: 1783590--1783881 Score: 423
Period size: 127 Copynumber: 2.4 Consensus size: 123
1783580 AAAAATGATT
* *
1783590 TAATAATAATTTA-AATAATGATT-TAATAATGAATTTAATAATAAATTTAATATTTAATGATTT
1 TAATAATGATTTATAATAATAATTATAATAATG-ATTTAATAATAAATTTAATATTTAATGATTT
*
1783653 GATGATTTAGTAATGATTTGATAAAAATCATTATAGTAATGATTCGATAATAATAATCATTA
65 GATGATTTAGTAATGATTTGATAAAAATCATTATAATAATGATT---TAATAATAATCATTA
* *
1783715 TAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAAT-GATTTAAATATTTAATGATT
1 TAATAATGATTTA-TAATAATAATTATAATAATGATTTAATAATAAATTT-AATATTTAATGATT
* *
1783779 TGATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTA
64 TGATGATTTAGTAATGATTTGATAAAAATCATTATAATAATGATTTAATAATAATCATTA
*
1783839 TAATAATGA-TT-TAATAATAATGATAATAATGATTTAATAATAA
1 TAATAATGATTTATAATAATAATTATAATAATGATTTAATAATAA
1783882 TAATGATAAT
Statistics
Matches: 153, Mismatches: 9, Indels: 13
0.87 0.05 0.07
Matches are distributed among these distances:
121 28 0.18
123 2 0.01
124 23 0.15
125 12 0.08
126 4 0.03
127 76 0.50
128 8 0.05
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (123 bp):
TAATAATGATTTATAATAATAATTATAATAATGATTTAATAATAAATTTAATATTTAATGATTTG
ATGATTTAGTAATGATTTGATAAAAATCATTATAATAATGATTTAATAATAATCATTA
Found at i:1783818 original size:3 final size:3
Alignment explanation
Indices: 1783800--1783894 Score: 52
Period size: 3 Copynumber: 32.7 Consensus size: 3
1783790 TAATGATTTG
* * * * * * * *
1783800 ATA ATA ATC ATT ATA ATA ATG AT- TTA GTA ATA ATC ATT ATA ATA ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
1783847 AT- TTA ATA ATA ATG ATA ATA ATG AT- TTA ATA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1783893 AT
1 AT
1783895 GATTTAATAG
Statistics
Matches: 69, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
2 3 0.04
3 66 0.96
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:1783854 original size:49 final size:49
Alignment explanation
Indices: 1783703--1783971 Score: 242
Period size: 49 Copynumber: 5.4 Consensus size: 49
1783693 GATTCGATAA
* * *
1783703 TAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAATGATT
1 TAATAATAATTATAATAATGATTTAATAATAATAATTATAATAATGATT
* * * * *
1783752 TAATAATGATT-T-A-AAT-ATTTAATGATTTGATGATT-TAGTAATGATTT
1 TAATAATAATTATAATAATGATTTAAT-A-ATAATAATTATAATAATGA-TT
* * *
1783799 GATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAATGATT
1 --TAATAATAATTATAATAATGATTTAATAATAATAATTATAATAATGATT
* *
1783850 TAATAATAATGATAATAATGATTTAATAATAATAATGATAATAATGATT
1 TAATAATAATTATAATAATGATTTAATAATAATAATTATAATAATGATT
* * * * *
1783899 TAATAGTAATTATTTAGTAATTATTTTATAATAATAATTTAATATTAATGATT
1 TAATAATAATTA--TAATAATGATTTAATAATAATAA-TT-ATAATAATGATT
*
1783952 TAATAATTATTACTAATAAT
1 TAATAATAATTA-TAATAAT
1783972 TACAGAATAA
Statistics
Matches: 178, Mismatches: 28, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
45 6 0.03
46 12 0.07
47 9 0.05
48 1 0.01
49 74 0.42
50 1 0.01
51 29 0.16
52 19 0.11
53 27 0.15
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (49 bp):
TAATAATAATTATAATAATGATTTAATAATAATAATTATAATAATGATT
Found at i:1783866 original size:9 final size:9
Alignment explanation
Indices: 1783852--1783897 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
1783842 TAATGATTTA
1783852 ATAATAATG
1 ATAATAATG
1783861 ATAATAATG
1 ATAATAATG
* *
1783870 AT-TTAATA
1 ATAATAATG
1783878 ATAATAATG
1 ATAATAATG
1783887 ATAATAATG
1 ATAATAATG
1783896 AT
1 AT
1783898 TTAATAGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
8 6 0.19
9 26 0.81
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (9 bp):
ATAATAATG
Found at i:1783883 original size:127 final size:123
Alignment explanation
Indices: 1783652--1783958 Score: 348
Period size: 127 Copynumber: 2.4 Consensus size: 123
1783642 TTTAATGATT
* *
1783652 TGATGATTTAGTAATGATTTGATAAAAATCATTATAGTAATGATTCGATAATAATAATCATTATA
1 TGATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATT---TAATAATAATCATTATA
* * * * * *
1783717 ATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATGAT-TTAAAT-ATTTAATGATT
63 ATAATGATTTAATAATAATCATAATAATAATAATATAATAATGATAAT-AATGATTTAAT-A-G
*
1783779 TGATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATA
1 TGATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATAATCATTATAATA
* *
1783844 ATGATTTAATAATAATGATAATAATGATTTAATAATAATAATGATAATAATGATTTAATAG
66 ATGATTTAATAATAATCATAATAAT-A-ATAAT-ATAATAATGATAATAATGATTTAATAG
* * * * * *
1783905 TAATTATTTAGTAATTATTTTATAATAATAATTTAATATTAATGATTTAATAAT
1 TGATGATTTAGTAATGATTTGATAATAATCA-TT-ATAATAATGATTTAATAAT
1783959 TATTACTAAT
Statistics
Matches: 155, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
124 41 0.26
125 1 0.01
126 29 0.19
127 59 0.38
128 25 0.16
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (123 bp):
TGATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATAATCATTATAATA
ATGATTTAATAATAATCATAATAATAATAATATAATAATGATAATAATGATTTAATAG
Found at i:1783902 original size:17 final size:17
Alignment explanation
Indices: 1783856--1783888 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1783846 GATTTAATAA
*
1783856 TAATGATAATAATGATT
1 TAATAATAATAATGATT
1783873 TAATAATAATAATGAT
1 TAATAATAATAATGAT
1783889 AATAATGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (17 bp):
TAATAATAATAATGATT
Found at i:1783903 original size:98 final size:96
Alignment explanation
Indices: 1783702--1783963 Score: 287
Period size: 98 Copynumber: 2.6 Consensus size: 96
1783692 TGATTCGATA
* *
1783702 ATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATGATTTAAA
1 ATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATAATTAAAA
* * * *
1783767 TATTTAATGATTTGATGATTTAGTAATGATTT
66 TATTTAATAATATAATGA-TTAATAATGATTT
1783799 GATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATAATGATA
1 -ATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATAAT--TA
1783864 ATAATGATTTAATAATAATAATGA-TAATAATGATTT
63 A-AAT-ATTTAATAAT-ATAATGATTAATAATGATTT
* * * * * * *
1783900 AATAGTAATTATT-TAGTAATTATTTTA-TAATAATAATTTAATATTAATGATTTAATAATTATT
1 -ATAATAATCATTATAATAATGA-TTTAGTAATAATCA-TT-ATAATAATGATTTAATAATAATT
1783963 A
62 A
1783964 CTAATAATTA
Statistics
Matches: 142, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
98 59 0.42
100 19 0.13
101 30 0.21
102 29 0.20
103 5 0.04
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.45
Consensus pattern (96 bp):
ATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATAATTAAAA
TATTTAATAATATAATGATTAATAATGATTT
Found at i:1783939 original size:39 final size:39
Alignment explanation
Indices: 1783787--1783962 Score: 137
Period size: 39 Copynumber: 4.6 Consensus size: 39
1783777 TTTGATGATT
* * * * *
1783787 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAG
1 TAGTAATGATTTAATAATTAT-TTTATAATAATAATTTAA
* * * *
1783827 TAATAATCATTATAATAATGA--TT-TAATAATAA--TGA
1 TAGTAATGATT-TAATAATTATTTTATAATAATAATTTAA
* * * * *
1783862 TAATAATGATTTAATAATAATAATGATAATAATGATTTAA
1 TAGTAATGATTTAATAATTAT-TTTATAATAATAATTTAA
* *
1783902 TAGTAATTATTTAGTAATTATTTTATAATAATAATTTAA
1 TAGTAATGATTTAATAATTATTTTATAATAATAATTTAA
*
1783941 TATTAATGATTTAATAATTATT
1 TAGTAATGATTTAATAATTATT
1783963 ACTAATAATT
Statistics
Matches: 107, Mismatches: 22, Indels: 15
0.74 0.15 0.10
Matches are distributed among these distances:
34 8 0.07
35 11 0.10
37 9 0.08
38 10 0.09
39 34 0.32
40 28 0.26
41 7 0.07
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.45
Consensus pattern (39 bp):
TAGTAATGATTTAATAATTATTTTATAATAATAATTTAA
Found at i:1783947 original size:11 final size:11
Alignment explanation
Indices: 1783827--1783882 Score: 58
Period size: 12 Copynumber: 4.9 Consensus size: 11
1783817 AATGATTTAG
*
1783827 TAATAATCATT
1 TAATAATAATT
*
1783838 ATAATAATGATT
1 -TAATAATAATT
*
1783850 TAATAATAATGA
1 TAATAATAAT-T
*
1783862 TAATAATGATT
1 TAATAATAATT
1783873 TAATAATAAT
1 TAATAATAAT
1783883 AATGATAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
11 18 0.49
12 19 0.51
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (11 bp):
TAATAATAATT
Found at i:1784123 original size:24 final size:24
Alignment explanation
Indices: 1784075--1784119 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1784065 GATTTGATAC
*
1784075 TAATGATTTACTAATTATTATTAA
1 TAATGATTTACTAATTAATATTAA
*
1784099 TAATGATTTA-TTATTAATATT
1 TAATGATTTACTAATTAATATT
1784120 TAATTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
TAATGATTTACTAATTAATATTAA
Found at i:1784126 original size:17 final size:17
Alignment explanation
Indices: 1784086--1784127 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1784076 AATGATTTAC
1784086 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
1784103 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
1784120 TAATTATT
1 TAATTATT
1784128 TGATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:1786300 original size:21 final size:22
Alignment explanation
Indices: 1786275--1786322 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1786265 ACAACTAATA
*
1786275 AACTATTC-TTAATATAACTTT
1 AACTATTCTTTAATATAACGTT
1786296 AACTATTCTTTAATATAACGTT
1 AACTATTCTTTAATATAACGTT
1786318 AACTA
1 AACTA
1786323 ATAAACTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.44
Consensus pattern (22 bp):
AACTATTCTTTAATATAACGTT
Found at i:1786338 original size:30 final size:29
Alignment explanation
Indices: 1786304--1786373 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 29
1786294 TTAACTATTC
*
1786304 TTTAATATAACGTT-AACTAATAAACTGTTT
1 TTTAATATAAC-TTAAACTAATAAA-TGATT
1786334 TTTAATATAACTTAAACTAATAAATGATT
1 TTTAATATAACTTAAACTAATAAATGATT
1786363 TTTAATTATAA
1 TTTAA-TATAA
1786374 TTTATTACTA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 11 0.30
30 26 0.70
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (29 bp):
TTTAATATAACTTAAACTAATAAATGATT
Found at i:1786502 original size:40 final size:36
Alignment explanation
Indices: 1786449--1786561 Score: 95
Period size: 40 Copynumber: 2.9 Consensus size: 36
1786439 CTTAACTATT
1786449 TAACTAAC--ACAAACTAATTACATATTTTTTATATA
1 TAACTAACAAACAAACTAATTA-ATATTTTTTATATA
*
1786484 TAACTAACGAATAACAAACTAACTAATTATTTTTATTAATATA
1 TAACTAAC--A-AACAAACTAATTAA-TA-TTTT-TT-ATATA
* *
1786527 TAACTATCAAACATACTAATTAAATAATTTTTTAT
1 TAACTAACAAACAAACTAATT-AAT-ATTTTTTAT
1786562 TTCTATATGA
Statistics
Matches: 63, Mismatches: 4, Indels: 19
0.73 0.05 0.22
Matches are distributed among these distances:
35 8 0.13
38 2 0.03
39 3 0.05
40 28 0.44
41 8 0.13
42 2 0.03
43 12 0.19
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.40
Consensus pattern (36 bp):
TAACTAACAAACAAACTAATTAATATTTTTTATATA
Found at i:1786691 original size:18 final size:18
Alignment explanation
Indices: 1786638--1786691 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 18
1786628 TTGTTTTACC
*
1786638 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
1786656 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
1786668 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
1786685 CTAATTT
1 CTAATTT
1786692 TAATAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 14
0.65 0.02 0.33
Matches are distributed among these distances:
11 3 0.11
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.11
16 2 0.07
17 2 0.07
18 10 0.36
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:1787246 original size:11 final size:11
Alignment explanation
Indices: 1787230--1787288 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
1787220 CTGAAGGACT
1787230 GCAATAATGCA
1 GCAATAATGCA
* *
1787241 GCAATAAGGGCT
1 GCAATAA-TGCA
1787253 GCAATAATGCA
1 GCAATAATGCA
* *
1787264 GCAATAAGTACT
1 GCAATAA-TGCA
1787276 GCAATAATGCA
1 GCAATAATGCA
1787287 GC
1 GC
1787289 TGAATTCACG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 20 0.53
12 18 0.47
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (11 bp):
GCAATAATGCA
Found at i:1787254 original size:23 final size:23
Alignment explanation
Indices: 1787223--1787288 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
1787213 ACGTGAGCTG
1787223 AAGGACTGCAATAATGCAGCAAT
1 AAGGACTGCAATAATGCAGCAAT
*
1787246 AAGGGCTGCAATAATGCAGCAAT
1 AAGGACTGCAATAATGCAGCAAT
*
1787269 AAGTACTGCAATAATGCAGC
1 AAGGACTGCAATAATGCAGC
1787289 TGAATTCACG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (23 bp):
AAGGACTGCAATAATGCAGCAAT
Found at i:1787258 original size:12 final size:12
Alignment explanation
Indices: 1787228--1787282 Score: 60
Period size: 12 Copynumber: 4.8 Consensus size: 12
1787218 AGCTGAAGGA
1787228 CTGCAATAA-TG
1 CTGCAATAAGTG
* *
1787239 CAGCAATAAGGG
1 CTGCAATAAGTG
1787251 CTGCAATAA-TG
1 CTGCAATAAGTG
* *
1787262 CAGCAATAAGTA
1 CTGCAATAAGTG
1787274 CTGCAATAA
1 CTGCAATAA
1787283 TGCAGCTGAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
11 17 0.49
12 18 0.51
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (12 bp):
CTGCAATAAGTG
Found at i:1787477 original size:29 final size:29
Alignment explanation
Indices: 1787445--1787523 Score: 122
Period size: 29 Copynumber: 2.7 Consensus size: 29
1787435 ATCAGGATGT
1787445 CGGGCTTGCATGGCGACCTATAAGGACGC
1 CGGGCTTGCATGGCGACCTATAAGGACGC
* *
1787474 CGGGATTGCATGGTGACCTATAAGGACGC
1 CGGGCTTGCATGGCGACCTATAAGGACGC
* *
1787503 CGGGCGTACATGGCGACCTAT
1 CGGGCTTGCATGGCGACCTAT
1787524 GTTGGTTCGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.22, C:0.25, G:0.34, T:0.19
Consensus pattern (29 bp):
CGGGCTTGCATGGCGACCTATAAGGACGC
Found at i:1787823 original size:23 final size:23
Alignment explanation
Indices: 1787792--1787878 Score: 138
Period size: 23 Copynumber: 3.8 Consensus size: 23
1787782 ACGTGAGCTG
* *
1787792 AAGGACTGCAATAATGCAGCAAT
1 AAGGGCTGCAATAATGCAACAAT
*
1787815 AAGGGCTGCAATAATACAACAAT
1 AAGGGCTGCAATAATGCAACAAT
1787838 AAGGGCTGCAATAATGCAACAAT
1 AAGGGCTGCAATAATGCAACAAT
*
1787861 AAGTGCTGCAATAATGCA
1 AAGGGCTGCAATAATGCA
1787879 GCTGAATTCA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.18
Consensus pattern (23 bp):
AAGGGCTGCAATAATGCAACAAT
Found at i:1788069 original size:29 final size:29
Alignment explanation
Indices: 1788037--1788115 Score: 140
Period size: 29 Copynumber: 2.7 Consensus size: 29
1788027 ATTAGGATGT
*
1788037 CGGGCGTGCATGACGACCTATAAGGACGC
1 CGGGCGTGCATGGCGACCTATAAGGACGC
*
1788066 CGGGCTTGCATGGCGACCTATAAGGACGC
1 CGGGCGTGCATGGCGACCTATAAGGACGC
1788095 CGGGCGTGCATGGCGACCTAT
1 CGGGCGTGCATGGCGACCTAT
1788116 GTTGGTTCGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.20, C:0.28, G:0.35, T:0.16
Consensus pattern (29 bp):
CGGGCGTGCATGGCGACCTATAAGGACGC
Found at i:1788352 original size:592 final size:592
Alignment explanation
Indices: 1787223--1788365 Score: 2124
Period size: 592 Copynumber: 1.9 Consensus size: 592
1787213 ACGTGAGCTG
* * *
1787223 AAGGACTGCAATAATGCAGCAATAAGGGCTGCAATAATGCAGCAATAAGTACTGCAATAATGCAG
1 AAGGACTGCAATAATACAACAATAAGGGCTGCAATAATGCAACAATAAGTACTGCAATAATGCAG
1787288 CTGAATTCACGCTGCATGCGAGCAGAGGTTTGCCGAGAGCAGAACACGTGAACAAAGCTTGGCGA
66 CTGAATTCACGCTGCATGCGAGCAGAGGTTTGCCGAGAGCAGAACACGTGAACAAAGCTTGGCGA
*
1787353 CCTATCCCATACCCCGTGCATGGCCCATGCATAGCACCAAAGCAGAGCAGCAGCTGGGCAGAGTA
131 CCTATCCCATACCCCGTGCATGGCCCATGCATAGCACCAAAGCAGAGCAGCAGCCGGGCAGAGTA
* *
1787418 GCAGAATCACGAGAACTATCAGGATGTCGGGCTTGCATGGCGACCTATAAGGACGCCGGGATTGC
196 GCAGAATCACGAGAACTATCAGGATGTCGGGCGTGCATGACGACCTATAAGGACGCCGGGATTGC
* *
1787483 ATGGTGACCTATAAGGACGCCGGGCGTACATGGCGACCTATGTTGGTTCGTCTGGATGTTGCCAC
261 ATGGCGACCTATAAGGACGCCGGGCGTACATGGCGACCTATGTTGGTTCGTCTAGATGTTGCCAC
*
1787548 GTCGTAGGTCGCCCGGATGGCATGGCGAGCTACGACCATCACTGTAGAATTTACCCCATTTGAGC
326 GTCGTAGGTCGCCCGGATGGCATGGCGAGCTACGACCATCACTGTAGAATTTACCCCATTTGAAC
1787613 AATTAATCTGAGCACTACATTATCTCGTGAAATAAAAACTTCGAGAGCATTATCTCGTTGATTTT
391 AATTAATCTGAGCACTACATTATCTCGTGAAATAAAAACTTCGAGAGCATTATCTCGTTGATTTT
1787678 GCCTTTTCTTATCACTCAAATCGCTTCATTCTATTACTTATATTAAATTACCTAATTGAGTGATA
456 GCCTTTTCTTATCACTCAAATCGCTTCATTCTATTACTTATATTAAATTACCTAATTGAGTGATA
1787743 ACGAAACTATTGAAGTGTTAATCTGCGTTATGGCCATTCACGTGAGCTGAAGGACTGCAATAATG
521 ACGAAACTATTGAAGTGTTAATCTGCGTTATGGCCATTCACGTGAGCTGAAGGACTGCAATAATG
1787808 CAGCAAT
586 CAGCAAT
* *
1787815 AAGGGCTGCAATAATACAACAATAAGGGCTGCAATAATGCAACAATAAGTGCTGCAATAATGCAG
1 AAGGACTGCAATAATACAACAATAAGGGCTGCAATAATGCAACAATAAGTACTGCAATAATGCAG
1787880 CTGAATTCACGCTGCATGCGAGCAGAGGTTTGCCGAGAGCAGAACACGTGAACAAAGCTTGGCGA
66 CTGAATTCACGCTGCATGCGAGCAGAGGTTTGCCGAGAGCAGAACACGTGAACAAAGCTTGGCGA
*
1787945 CCTATCCCATGCCCCGTGCATGGCCCATGCATAGCACCAAAGCAGAGCAGCAGCCGGGCAGAGTA
131 CCTATCCCATACCCCGTGCATGGCCCATGCATAGCACCAAAGCAGAGCAGCAGCCGGGCAGAGTA
* *
1788010 GCAGAATCACGAGAACTATTAGGATGTCGGGCGTGCATGACGACCTATAAGGACGCCGGGCTTGC
196 GCAGAATCACGAGAACTATCAGGATGTCGGGCGTGCATGACGACCTATAAGGACGCCGGGATTGC
*
1788075 ATGGCGACCTATAAGGACGCCGGGCGTGCATGGCGACCTATGTTGGTTCGTCTAGATGTTGCCAC
261 ATGGCGACCTATAAGGACGCCGGGCGTACATGGCGACCTATGTTGGTTCGTCTAGATGTTGCCAC
1788140 GTCGTAGGTCGCCCGGATGGCATGGCGAGCTACGACCATCACTGTAGAATTTACCCCATTTGAAC
326 GTCGTAGGTCGCCCGGATGGCATGGCGAGCTACGACCATCACTGTAGAATTTACCCCATTTGAAC
* *
1788205 AATTAATCTGAGCACTGCATTATCTCGTGAAATAAAAACTTCGAGAGGATTATCTCGTTGATTTT
391 AATTAATCTGAGCACTACATTATCTCGTGAAATAAAAACTTCGAGAGCATTATCTCGTTGATTTT
*
1788270 GCCTTTTCTTATCACTCAAATCGCTTCGTTCTATTACTTATATTAAATTACCTAATTGAGTGATA
456 GCCTTTTCTTATCACTCAAATCGCTTCATTCTATTACTTATATTAAATTACCTAATTGAGTGATA
1788335 ACGAAACTATTGAAGTGTTAATCTGCGTTAT
521 ACGAAACTATTGAAGTGTTAATCTGCGTTAT
1788366 TATGTACGTA
Statistics
Matches: 533, Mismatches: 18, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
592 533 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.25
Consensus pattern (592 bp):
AAGGACTGCAATAATACAACAATAAGGGCTGCAATAATGCAACAATAAGTACTGCAATAATGCAG
CTGAATTCACGCTGCATGCGAGCAGAGGTTTGCCGAGAGCAGAACACGTGAACAAAGCTTGGCGA
CCTATCCCATACCCCGTGCATGGCCCATGCATAGCACCAAAGCAGAGCAGCAGCCGGGCAGAGTA
GCAGAATCACGAGAACTATCAGGATGTCGGGCGTGCATGACGACCTATAAGGACGCCGGGATTGC
ATGGCGACCTATAAGGACGCCGGGCGTACATGGCGACCTATGTTGGTTCGTCTAGATGTTGCCAC
GTCGTAGGTCGCCCGGATGGCATGGCGAGCTACGACCATCACTGTAGAATTTACCCCATTTGAAC
AATTAATCTGAGCACTACATTATCTCGTGAAATAAAAACTTCGAGAGCATTATCTCGTTGATTTT
GCCTTTTCTTATCACTCAAATCGCTTCATTCTATTACTTATATTAAATTACCTAATTGAGTGATA
ACGAAACTATTGAAGTGTTAATCTGCGTTATGGCCATTCACGTGAGCTGAAGGACTGCAATAATG
CAGCAAT
Found at i:1789450 original size:31 final size:31
Alignment explanation
Indices: 1789412--1789475 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1789402 TTGACCTCTA
* *
1789412 TTTTTTAATATTTTA-ACTCTTAATATTTTAT
1 TTTTTTAATATTATAGA-TCTCAATATTTTAT
1789443 TTTTTTAATATTATAGATCTCAATATTTTAT
1 TTTTTTAATATTATAGATCTCAATATTTTAT
1789474 TT
1 TT
1789476 ATTGGTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (31 bp):
TTTTTTAATATTATAGATCTCAATATTTTAT
Found at i:1789641 original size:31 final size:31
Alignment explanation
Indices: 1789603--1789675 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
1789593 TGTCAGTTTT
*
1789603 TTGAGTGACATAACACATACTATATTATATA
1 TTGAGTGACATAACACATACTATATCATATA
* * *
1789634 TTGAGTGACATAATACATATTATATCATATT
1 TTGAGTGACATAACACATACTATATCATATA
1789665 TTGAGTGACAT
1 TTGAGTGACAT
1789676 GTTACAAGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.38
Consensus pattern (31 bp):
TTGAGTGACATAACACATACTATATCATATA
Found at i:1789811 original size:60 final size:61
Alignment explanation
Indices: 1789745--1789861 Score: 191
Period size: 61 Copynumber: 1.9 Consensus size: 61
1789735 TTCTTTCTAG
* * *
1789745 CATGAGATATTTTGATAAAAA-TAAAATATTAAAAAGTAGAATACTCCAAAATAAAAAAGT
1 CATGAGATATCTTAATAAAAATTAAAATATTAAAAACTAGAATACTCCAAAATAAAAAAGT
*
1789805 CATGAGATATCTTAATAAAAATTAAAATATTAAAAACTAGAATATTCCAAAATAAAA
1 CATGAGATATCTTAATAAAAATTAAAATATTAAAAACTAGAATACTCCAAAATAAAA
1789862 CTAATAGTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 19 0.37
61 33 0.63
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.27
Consensus pattern (61 bp):
CATGAGATATCTTAATAAAAATTAAAATATTAAAAACTAGAATACTCCAAAATAAAAAAGT
Found at i:1791288 original size:22 final size:24
Alignment explanation
Indices: 1791263--1791312 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 24
1791253 TAAGTTTTTC
1791263 TTATATATTT-T-TCATTAAAAAT
1 TTATATATTTGTCTCATTAAAAAT
*
1791285 TTAT-T-TTTGTCTCATTTAAAAT
1 TTATATATTTGTCTCATTAAAAAT
1791307 TT-TATA
1 TTATATA
1791313 AGTTTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
20 3 0.13
21 3 0.13
22 17 0.74
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (24 bp):
TTATATATTTGTCTCATTAAAAAT
Found at i:1792568 original size:23 final size:24
Alignment explanation
Indices: 1792524--1792571 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1792514 ACTTTACAAA
1792524 TTTAAATTATGTAAAAAATAAGTT
1 TTTAAATTATGTAAAAAATAAGTT
*
1792548 TTTAAATTATGT-GAAAATAAGTT
1 TTTAAATTATGTAAAAAATAAGTT
1792571 T
1 T
1792572 ACAAATACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (24 bp):
TTTAAATTATGTAAAAAATAAGTT
Found at i:1792577 original size:23 final size:24
Alignment explanation
Indices: 1792527--1792577 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
1792517 TTACAAATTT
**
1792527 AAATTATGTAAAAAATAAGTTTTT
1 AAATTATGTAAAAAATAAGTTTAC
*
1792551 AAATTATGT-GAAAATAAGTTTAC
1 AAATTATGTAAAAAATAAGTTTAC
1792574 AAAT
1 AAAT
1792578 ACACATATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (24 bp):
AAATTATGTAAAAAATAAGTTTAC
Found at i:1793242 original size:20 final size:20
Alignment explanation
Indices: 1793213--1793255 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1793203 AACAGACACA
1793213 CCTAACCAAATAAAACCACT
1 CCTAACCAAATAAAACCACT
*
1793233 CCTAAGCAAATAAAACCACT
1 CCTAACCAAATAAAACCACT
1793253 CCT
1 CCT
1793256 CTCTAATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.35, G:0.02, T:0.16
Consensus pattern (20 bp):
CCTAACCAAATAAAACCACT
Found at i:1797696 original size:33 final size:33
Alignment explanation
Indices: 1797658--1797736 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
1797648 CGTTTTTAAG
1797658 CGCCGCTAAAAGCACTTGCGACGATAGAAAAAA
1 CGCCGCTAAAAGCACTTGCGACGATAGAAAAAA
*
1797691 CGCCGCTAAAAGCACTTGCGACGATAGGAAAAA
1 CGCCGCTAAAAGCACTTGCGACGATAGAAAAAA
*
1797724 CGCCGCAAAAAGC
1 CGCCGCTAAAAGC
1797737 GCCGATAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.41, C:0.27, G:0.23, T:0.10
Consensus pattern (33 bp):
CGCCGCTAAAAGCACTTGCGACGATAGAAAAAA
Found at i:1797833 original size:43 final size:43
Alignment explanation
Indices: 1797783--1798195 Score: 284
Period size: 43 Copynumber: 9.3 Consensus size: 43
1797773 TTAGAACAAA
* * * * * *
1797783 AAACGCCGCAATAGGTCAAGATCTATCGTGGCGTTTTTGCAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
1797826 AAACGCCGCAAAAGGTCGATATCTATAGCGGCAG-TTTTGGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGC-GTTTTTGGAAC
** *
1797869 AAACGCAACAAAATGTCGATATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
* * * * * *
1797912 AAACGCCGCAAAATGTTTAGATAAAGGTCAGATCTATAGCGACGCTTTCGGAAT
1 AAACGCCGCAAAA-G----G-T---CG--ATATCTATAGCGGCGTTTTTGGAAC
* * *
1797966 AAACGCCGCAAAAGGTC-AGATCTATAGCGACGTTTTTGGATAT
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGA-AC
* * ** * **
1798009 AAACGCCGCAAAAGATC-AGATCTATAGTAGCATTTTTTAATAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGA-AC
* *
1798052 AAATGCCGCAAAAGGTCAGAT-T-TATAGCGGTGTTTTTGGATAC
1 AAACGCCGCAAAAGGTC-GATATCTATAGCGGCGTTTTTGGA-AC
* *
1798095 AAACGCCGTAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGA-AC
* * * * *
1798138 AAACGCCGTAAAAGATC-AAATCTATAACGGCGGTTTTT-TACAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGC-GTTTTTGGA-AC
*
1798181 AAACGCTGCAAAAGG
1 AAACGCCGCAAAAGG
1798196 GCTCATGATA
Statistics
Matches: 301, Mismatches: 50, Indels: 38
0.77 0.13 0.10
Matches are distributed among these distances:
41 1 0.00
42 23 0.08
43 229 0.76
44 8 0.03
45 1 0.00
48 2 0.01
49 2 0.01
52 1 0.00
53 1 0.00
54 33 0.11
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
Found at i:1797978 original size:97 final size:98
Alignment explanation
Indices: 1797836--1798021 Score: 243
Period size: 97 Copynumber: 1.9 Consensus size: 98
1797826 AAACGCCGCA
* * * * * *
1797836 AAAGGTCGATATCTATAGCGGCAGTTTTGGAACAAACGCAACAAAATGTCGATATCTATAGCGGC
1 AAAGGTCGAGATCTATAGCGACAGTTTCGGAACAAACGCAACAAAAGGTC-AGATCTATAGCGAC
1797901 GTTTTTGGA-ACAAACGCCGCAAAATGTTTAGAT
65 GTTTTTGGATACAAACGCCGCAAAATGTTTAGAT
* **
1797934 AAAGGTC-AGATCTATAGCGAC-GCTTTCGGAATAAACGCCGCAAAAGGTCAGATCTATAGCGAC
1 AAAGGTCGAGATCTATAGCGACAG-TTTCGGAACAAACGCAACAAAAGGTCAGATCTATAGCGAC
*
1797997 GTTTTTGGATATAAACGCCGCAAAA
65 GTTTTTGGATACAAACGCCGCAAAA
1798022 GATCAGATCT
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
96 22 0.29
97 47 0.62
98 7 0.09
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.24
Consensus pattern (98 bp):
AAAGGTCGAGATCTATAGCGACAGTTTCGGAACAAACGCAACAAAAGGTCAGATCTATAGCGACG
TTTTTGGATACAAACGCCGCAAAATGTTTAGAT
Found at i:1798175 original size:129 final size:128
Alignment explanation
Indices: 1797934--1798195 Score: 335
Period size: 129 Copynumber: 2.0 Consensus size: 128
1797924 ATGTTTAGAT
*
1797934 AAAGGTCAGATCTATAGCGACGCTTTCGGAATAAACGCCGCAAAAGGTCAGATCTATAGCGACGT
1 AAAGGTCAGATCTATAGCGACGCTTTCGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGACGT
* * ** * * *
1797999 TTTTGGATATAAACGCCGCAAAAGATCAGATCTATAGTAGCATTTTTTAATACAAATGCCGCA
66 TTTTGGATACAAACGCCGCAAAAGATCAAATCTATAACAGCAGTTTTTAACACAAACGCCGCA
* ** * * * *
1798062 AAAGGTCAGATTTATAGCGGTGTTTTTGGATACAAACGCCGTAAAAGGTCAGATCTATAGCGGCG
1 AAAGGTCAGATCTATAGCGACGCTTTCGGA-ACAAACGCCGCAAAAGGTCAGATCTATAGCGACG
* * * * *
1798127 TTTTTGGATACAAACGCCGTAAAAGATCAAATCTATAACGGCGGTTTTTTACACAAACGCTGCA
65 TTTTTGGATACAAACGCCGCAAAAGATCAAATCTATAACAGCAGTTTTTAACACAAACGCCGCA
1798191 AAAGG
1 AAAGG
1798196 GCTCATGATA
Statistics
Matches: 113, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
128 25 0.22
129 88 0.78
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (128 bp):
AAAGGTCAGATCTATAGCGACGCTTTCGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGACGT
TTTTGGATACAAACGCCGCAAAAGATCAAATCTATAACAGCAGTTTTTAACACAAACGCCGCA
Found at i:1799805 original size:22 final size:22
Alignment explanation
Indices: 1799777--1799836 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
1799767 ATTTACACAT
1799777 AGTGTACCGATGCACCATTAAG
1 AGTGTACCGATGCACCATTAAG
*
1799799 AGTGTACCGATGCACCATTGAG
1 AGTGTACCGATGCACCATTAAG
1799821 AGTGTACCGATGCACC
1 AGTGTACCGATGCACC
1799837 CACGCTCCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (22 bp):
AGTGTACCGATGCACCATTAAG
Found at i:1805558 original size:44 final size:44
Alignment explanation
Indices: 1805494--1805594 Score: 130
Period size: 44 Copynumber: 2.3 Consensus size: 44
1805484 TTTTGTGCAC
* * * *
1805494 TATGCATTGATACACCATGAAAGTGTATCGATGCATCCCTTGAA
1 TATGCATCGATACAACATGAAAGTGCACCGATGCATCCCTTGAA
* * *
1805538 TATGCATCGATACAATATGAAGGTGCACCGATGCATTCCTTGAA
1 TATGCATCGATACAACATGAAAGTGCACCGATGCATCCCTTGAA
*
1805582 TGTGCATCGATAC
1 TATGCATCGATAC
1805595 CCTATGTAGT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (44 bp):
TATGCATCGATACAACATGAAAGTGCACCGATGCATCCCTTGAA
Found at i:1807624 original size:8 final size:9
Alignment explanation
Indices: 1807597--1807635 Score: 69
Period size: 9 Copynumber: 4.3 Consensus size: 9
1807587 AATTCCTTCA
*
1807597 TTTGTATTT
1 TTTGGATTT
1807606 TTTGGATTT
1 TTTGGATTT
1807615 TTTGGATTT
1 TTTGGATTT
1807624 TTTGGATTT
1 TTTGGATTT
1807633 TTT
1 TTT
1807636 ATCTTTTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.10, C:0.00, G:0.18, T:0.72
Consensus pattern (9 bp):
TTTGGATTT
Found at i:1824547 original size:11 final size:12
Alignment explanation
Indices: 1824533--1824562 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
1824523 ATAACTAAGT
1824533 AATAAAATAA-A
1 AATAAAATAACA
1824544 AATAAAATAACA
1 AATAAAATAACA
1824556 AATAAAA
1 AATAAAA
1824563 GCAATCATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (12 bp):
AATAAAATAACA
Found at i:1825508 original size:20 final size:20
Alignment explanation
Indices: 1825483--1825536 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1825473 TTGCTGGAAT
*
1825483 TTAAGACAAAGAAACAATGA
1 TTAAGACAATGAAACAATGA
*
1825503 TTAAGACAATGAAATAATGA
1 TTAAGACAATGAAACAATGA
1825523 TTAAGACAATGAAA
1 TTAAGACAATGAAA
1825537 AAAAGGGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.57, C:0.07, G:0.15, T:0.20
Consensus pattern (20 bp):
TTAAGACAATGAAACAATGA
Found at i:1828047 original size:55 final size:55
Alignment explanation
Indices: 1827882--1828196 Score: 350
Period size: 55 Copynumber: 5.8 Consensus size: 55
1827872 TCAATTACCA
* * * * * *
1827882 TATTGGCACTATGTGTGCAA-CCTAAGTAATTAATAATTAGTTTGTGAATTACCG
1 TATTGGCACTATGTGTGCAACCCCAAGAAATTCATAATGAGTTTATGAATTTCCG
* * * * * *
1827936 TATTGGCACTATGTGTGCAA-CCTAAGTAATTCATAATTAATTTGTGAATTACCG
1 TATTGGCACTATGTGTGCAACCCCAAGAAATTCATAATGAGTTTATGAATTTCCG
* * *
1827990 TATTGGCACTATGTGTGGAACCCCACA-AAATTCATAATGAATTTATGAATTTTCG
1 TATTGGCACTATGTGTGCAACCCCA-AGAAATTCATAATGAGTTTATGAATTTCCG
* * * *
1828045 TATTGACATTATGTGTGCAACCCCAATAAATTCATAATGAGTTTATGAATTTCCA
1 TATTGGCACTATGTGTGCAACCCCAAGAAATTCATAATGAGTTTATGAATTTCCG
* ** * * *
1828100 TATTGGCATTATGTGCACAATCCCACA-AAATTCATAATGAGTTTATGAATTTTCA
1 TATTGGCACTATGTGTGCAACCCCA-AGAAATTCATAATGAGTTTATGAATTTCCG
*
1828155 TATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGT
1 TATTGGCACTATGTGTGCAACCCCAAGAAATTCATAATGAGT
1828197 ACTCTACTTT
Statistics
Matches: 231, Mismatches: 25, Indels: 9
0.87 0.09 0.03
Matches are distributed among these distances:
54 72 0.31
55 157 0.68
56 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (55 bp):
TATTGGCACTATGTGTGCAACCCCAAGAAATTCATAATGAGTTTATGAATTTCCG
Found at i:1832321 original size:25 final size:26
Alignment explanation
Indices: 1832293--1832346 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
1832283 AATAATCTTT
* *
1832293 TTTTATCTTT-TAAATTTTTATAAAA
1 TTTTATCTTTCTAAAATTTTAAAAAA
*
1832318 TTTTATTTTTCTAAAATTTTAAAAAA
1 TTTTATCTTTCTAAAATTTTAAAAAA
1832344 TTT
1 TTT
1832347 ATTTTATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTTATCTTTCTAAAATTTTAAAAAA
Found at i:1832327 original size:17 final size:16
Alignment explanation
Indices: 1832306--1832338 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1832296 TATCTTTTAA
1832306 ATTTTTATAAAATTTT
1 ATTTTTATAAAATTTT
*
1832322 ATTTTTCTAAAATTTT
1 ATTTTTATAAAATTTT
1832338 A
1 A
1832339 AAAAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTTATAAAATTTT
Found at i:1832347 original size:25 final size:25
Alignment explanation
Indices: 1832294--1832351 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
1832284 ATAATCTTTT
* * *
1832294 TTTATCTTTTAAATTTTTATAAAAT
1 TTTATTTTTTAAAATTTTATAAAAA
1832319 TTTATTTTTCTAAAATTTTA-AAAAA
1 TTTATTTTT-TAAAATTTTATAAAAA
1832344 TTTATTTT
1 TTTATTTT
1832352 ATAATATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 20 0.69
26 9 0.31
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTATTTTTTAAAATTTTATAAAAA
Found at i:1834908 original size:18 final size:18
Alignment explanation
Indices: 1834869--1835007 Score: 183
Period size: 18 Copynumber: 7.8 Consensus size: 18
1834859 TCATGCAAAC
* *
1834869 TAAATGGACTACCA-ACT
1 TAAATGAACTAGCATACT
*
1834886 TAAATGAACTAGCATATT
1 TAAATGAACTAGCATACT
*
1834904 TAAAT-AACTAGCTTACT
1 TAAATGAACTAGCATACT
* * *
1834921 TAAATGAAATAACATTCT
1 TAAATGAACTAGCATACT
1834939 TAAATGAACTAGCATACT
1 TAAATGAACTAGCATACT
*
1834957 TAAATGAACTAGCATGCT
1 TAAATGAACTAGCATACT
1834975 TAAATGAACTAGCATACT
1 TAAATGAACTAGCATACT
*
1834993 TAAATGAACTTGCAT
1 TAAATGAACTAGCAT
1835008 CATGTGTAAT
Statistics
Matches: 105, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
17 27 0.26
18 78 0.74
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (18 bp):
TAAATGAACTAGCATACT
Found at i:1842212 original size:19 final size:17
Alignment explanation
Indices: 1842190--1842235 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
1842180 TGAAACAAAT
1842190 ATAAAAAAAATGAAATTGA
1 ATAAAAAAAAT-AAA-TGA
1842209 ATAAAATAAAATAAATGA
1 ATAAAA-AAAATAAATGA
*
1842227 AGAAAAAAA
1 ATAAAAAAA
1842236 TATATATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 8 0.32
19 9 0.36
20 5 0.20
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (17 bp):
ATAAAAAAAATAAATGA
Found at i:1842343 original size:22 final size:21
Alignment explanation
Indices: 1842324--1842375 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
1842314 AAACATAATG
1842324 AAAATAAATAAATAGTATAAAT
1 AAAATAAA-AAATAGTATAAAT
*
1842346 AAAATAAAAAATA--AAAAAT
1 AAAATAAAAAATAGTATAAAT
1842365 AAATATAAAAA
1 AAA-ATAAAAA
1842376 TATAAAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 8 0.29
20 7 0.25
21 5 0.18
22 8 0.29
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (21 bp):
AAAATAAAAAATAGTATAAAT
Found at i:1842358 original size:7 final size:7
Alignment explanation
Indices: 1842346--1842383 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
1842336 TAGTATAAAT
1842346 AAAATAA
1 AAAATAA
1842353 AAAATAA
1 AAAATAA
1842360 AAAAT-A
1 AAAATAA
*
1842366 AATATAA
1 AAAATAA
1842373 AAATATAA
1 AAA-ATAA
1842381 AAA
1 AAA
1842384 TGTATGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
6 5 0.19
7 15 0.56
8 7 0.26
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (7 bp):
AAAATAA
Found at i:1842363 original size:14 final size:14
Alignment explanation
Indices: 1842346--1842383 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
1842336 TAGTATAAAT
1842346 AAAATAAAAAATAA
1 AAAATAAAAAATAA
*
1842360 AAAAT-AAATATAA
1 AAAATAAAAAATAA
1842373 AAATATAAAAA
1 AAA-ATAAAAA
1842384 TGTATGTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 10 0.50
14 7 0.35
15 3 0.15
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAATAAAAAATAA
Found at i:1842364 original size:28 final size:29
Alignment explanation
Indices: 1842324--1842383 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
1842314 AAACATAATG
*
1842324 AAAATAAATAAAT-AGTATAAATAAAATAA
1 AAAATAAATAAATAAATATAAA-AAAATAA
*
1842353 AAAATAAA-AAATAAATATAAAAATATAA
1 AAAATAAATAAATAAATATAAAAAAATAA
1842381 AAA
1 AAA
1842384 TGTATGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.22
Consensus pattern (29 bp):
AAAATAAATAAATAAATATAAAAAAATAA
Found at i:1842366 original size:19 final size:21
Alignment explanation
Indices: 1842342--1842383 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 21
1842332 TAAATAGTAT
1842342 AAATAAA-ATAAAAA-ATAAA
1 AAATAAATATAAAAATATAAA
1842361 AAATAAATATAAAAATATAAA
1 AAATAAATATAAAAATATAAA
1842382 AA
1 AA
1842384 TGTATGTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 7 0.33
21 7 0.33
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (21 bp):
AAATAAATATAAAAATATAAA
Found at i:1842368 original size:18 final size:18
Alignment explanation
Indices: 1842324--1842384 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
1842314 AAACATAATG
* *
1842324 AAAATAAATAAATAGT-A
1 AAAATAAATAAAAAATAA
*
1842341 TAAATAAAATAAAAAATAA
1 AAAAT-AAATAAAAAATAA
1842360 AAAATAAATATAAAAATATA
1 AAAATAAATA-AAAAATA-A
1842380 AAAAT
1 AAAAT
1842385 GTATGTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.11
18 14 0.39
19 12 0.33
20 6 0.17
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (18 bp):
AAAATAAATAAAAAATAA
Found at i:1842571 original size:2 final size:2
Alignment explanation
Indices: 1842566--1842590 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1842556 ATAAAAAATA
1842566 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1842591 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1842652 original size:19 final size:18
Alignment explanation
Indices: 1842630--1842677 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
1842620 TATAACGCAA
1842630 ATAA-AAATGAAATAAAATT
1 ATAATAAAT-AAATAAAA-T
1842649 ATAATAAATAAATAAAAT
1 ATAATAAATAAATAAAAT
1842667 ATAATTAAATA
1 ATAA-TAAATA
1842678 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.19
19 18 0.67
20 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
ATAATAAATAAATAAAAT
Found at i:1843185 original size:37 final size:37
Alignment explanation
Indices: 1843092--1843193 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
1843082 ATGCTTGTGG
* * ** * * *
1843092 ATCCTATATTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
*
1843129 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTAT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
1843166 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
1843194 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
Found at i:1847791 original size:13 final size:13
Alignment explanation
Indices: 1847775--1847799 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1847765 TTCTGTTAAA
1847775 TTTTTATTTTTAC
1 TTTTTATTTTTAC
1847788 TTTTTATTTTTA
1 TTTTTATTTTTA
1847800 TTCGATCAAG
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:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTTTTAC
Found at i:1872877 original size:17 final size:17
Alignment explanation
Indices: 1872857--1872897 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1872847 TTGTGGCTTC
1872857 TTCTTTTATTATTTTTA
1 TTCTTTTATTATTTTTA
*
1872874 TTCTTTTATTATTTTTT
1 TTCTTTTATTATTTTTA
1872891 TTCTTTT
1 TTCTTTT
1872898 TGATGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (17 bp):
TTCTTTTATTATTTTTA
Found at i:1881745 original size:21 final size:21
Alignment explanation
Indices: 1881716--1881774 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1881706 CTTAGAAATG
*
1881716 TCCCAAAGGACCACATATATC
1 TCCCGAAGGACCACATATATC
* *
1881737 TCCCGAAGGACCCCATATATG
1 TCCCGAAGGACCACATATATC
* *
1881758 TCTCGAATGACCACATA
1 TCCCGAAGGACCACATA
1881775 GAATTCTTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.32, G:0.14, T:0.20
Consensus pattern (21 bp):
TCCCGAAGGACCACATATATC
Found at i:1881819 original size:23 final size:23
Alignment explanation
Indices: 1881770--1881820 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1881760 TCGAATGACC
* * *
1881770 ACATAGAATTCTTCTTAAGGACC
1 ACATAGAATTATCCTTAAGGACA
1881793 ACATAGAATTATCCTTTAA-GACA
1 ACATAGAATTATCC-TTAAGGACA
1881816 ACATA
1 ACATA
1881821 TATAATCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
ACATAGAATTATCCTTAAGGACA
Found at i:1893488 original size:28 final size:28
Alignment explanation
Indices: 1893452--1893510 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
1893442 TTATTGTAGT
1893452 GCATCAAGAAGTATATTTCTATACTGTA
1 GCATCAAGAAGTATATTTCTATACTGTA
1893480 GCATCAAGAAGTATATTTCTATACTGTA
1 GCATCAAGAAGTATATTTCTATACTGTA
1893508 GCA
1 GCA
1893511 GTCACTGTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (28 bp):
GCATCAAGAAGTATATTTCTATACTGTA
Found at i:1895647 original size:13 final size:13
Alignment explanation
Indices: 1895629--1895653 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1895619 TTTATAAAAA
1895629 AAAATAAAATAAT
1 AAAATAAAATAAT
1895642 AAAATAAAATAA
1 AAAATAAAATAA
1895654 ATCATCATTG
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:1897245 original size:19 final size:18
Alignment explanation
Indices: 1897221--1897274 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
1897211 GTGAAATATG
1897221 TAAATAAAAAAGAATTAAT
1 TAAATAAAAAA-AATTAAT
*
1897240 TAAAT-AAATAAATTAAT
1 TAAATAAAAAAAATTAAT
*
1897257 TAAGATAAATAAAATTAA
1 TAA-ATAAAAAAAATTAA
1897275 GAATATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 10 0.33
18 6 0.20
19 14 0.47
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (18 bp):
TAAATAAAAAAAATTAAT
Found at i:1898492 original size:48 final size:48
Alignment explanation
Indices: 1898422--1898518 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
1898412 TGAAAACTGA
1898422 CCCCCCTCAACAGCAATTCTTGAAGCCAATTTACACCCCTCTACAATC
1 CCCCCCTCAACAGCAATTCTTGAAGCCAATTTACACCCCTCTACAATC
1898470 CCCCCCTCAACAGCAATTCTTGAAGCCAATTTACACCCCTCTACAATC
1 CCCCCCTCAACAGCAATTCTTGAAGCCAATTTACACCCCTCTACAATC
1898518 C
1 C
1898519 GTATGGGATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.29, C:0.42, G:0.06, T:0.23
Consensus pattern (48 bp):
CCCCCCTCAACAGCAATTCTTGAAGCCAATTTACACCCCTCTACAATC
Found at i:1901151 original size:2 final size:2
Alignment explanation
Indices: 1901144--1901168 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1901134 TTAATCATTA
1901144 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1901169 ATGATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1903728 original size:12 final size:12
Alignment explanation
Indices: 1903655--1903728 Score: 55
Period size: 12 Copynumber: 6.1 Consensus size: 12
1903645 CGTCTTGTCT
1903655 TCTTTTTTCTTC
1 TCTTTTTTCTTC
*
1903667 ACTTTTTTCTT-
1 TCTTTTTTCTTC
*
1903678 TGTTTTTAT-TTC
1 TCTTTTT-TCTTC
*
1903690 TCTTTTTTATTTTC
1 TC-TTTTT-TCTTC
*
1903704 TCTTTGCTT-TTC
1 TCTTT-TTTCTTC
1903716 TCTTTTTTCTTC
1 TCTTTTTTCTTC
1903728 T
1 T
1903729 TTTCTCTTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
11 9 0.18
12 24 0.48
13 11 0.22
14 6 0.12
ACGTcount: A:0.04, C:0.19, G:0.03, T:0.74
Consensus pattern (12 bp):
TCTTTTTTCTTC
Found at i:1906866 original size:16 final size:17
Alignment explanation
Indices: 1906847--1906883 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1906837 GTGAAATATG
*
1906847 TAAATATAAAA-AAGAA
1 TAAATATAAAATAAAAA
1906863 TAAA-ATAAAATAAAAA
1 TAAATATAAAATAAAAA
1906879 TAAAT
1 TAAAT
1906884 TAATTCATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
TAAATATAAAATAAAAA
Found at i:1909594 original size:36 final size:35
Alignment explanation
Indices: 1909547--1909625 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 35
1909537 AATGATATTG
* *
1909547 ATGCTAATAATAAGTGATATCACTTGGTAAATACAT
1 ATGCTAATAATAAGTCATATCACTTGGTAAATA-AC
* *
1909583 ATGCTAATAATAAGTCATGTCACTTGGTGAATAAC
1 ATGCTAATAATAAGTCATATCACTTGGTAAATAAC
1909618 ATGCTAAT
1 ATGCTAAT
1909626 TTTTTTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 9 0.23
36 30 0.77
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (35 bp):
ATGCTAATAATAAGTCATATCACTTGGTAAATAAC
Found at i:1910252 original size:15 final size:15
Alignment explanation
Indices: 1910232--1910269 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1910222 ATCGGACATC
*
1910232 AAACATGGATTAATT
1 AAACATGGATCAATT
1910247 AAACATGGATCAATT
1 AAACATGGATCAATT
1910262 AAACATGG
1 AAACATGG
1910270 TTTTCTAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (15 bp):
AAACATGGATCAATT
Found at i:1917452 original size:27 final size:27
Alignment explanation
Indices: 1917422--1917482 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
1917412 AGCCGAGTCA
1917422 AACTCGAGTACTACTGAGCTCGACTCG
1 AACTCGAGTACTACTGAGCTCGACTCG
* *
1917449 AACTCGAGTACTGCTGAGCTCTACTCG
1 AACTCGAGTACTACTGAGCTCGACTCG
1917476 AACTCGA
1 AACTCGA
1917483 AAACTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (27 bp):
AACTCGAGTACTACTGAGCTCGACTCG
Found at i:1934682 original size:21 final size:21
Alignment explanation
Indices: 1934658--1934734 Score: 154
Period size: 21 Copynumber: 3.7 Consensus size: 21
1934648 TATGTCCAAC
1934658 AAAGGATCGATCCCTTGACCA
1 AAAGGATCGATCCCTTGACCA
1934679 AAAGGATCGATCCCTTGACCA
1 AAAGGATCGATCCCTTGACCA
1934700 AAAGGATCGATCCCTTGACCA
1 AAAGGATCGATCCCTTGACCA
1934721 AAAGGATCGATCCC
1 AAAGGATCGATCCC
1934735 AAACTTTCTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.18
Consensus pattern (21 bp):
AAAGGATCGATCCCTTGACCA
Found at i:1954136 original size:21 final size:19
Alignment explanation
Indices: 1954108--1954153 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
1954098 TCATTGAATC
1954108 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
1954128 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
1954147 ACTTAGT
1 A-TTAGT
1954154 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:1963027 original size:41 final size:41
Alignment explanation
Indices: 1962982--1963059 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1962972 AATAATTAGC
* * *
1962982 ATGAATTTAAATTATGGTTGCGTTGGGTTTAATATGACTAA
1 ATGAACTTAAATTAAGATTGCGTTGGGTTTAATATGACTAA
* *
1963023 ATGAACTTAAATTAAGATTGCGTTGTGTTTTATATGA
1 ATGAACTTAAATTAAGATTGCGTTGGGTTTAATATGA
1963060 TTATGATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (41 bp):
ATGAACTTAAATTAAGATTGCGTTGGGTTTAATATGACTAA
Found at i:1971724 original size:3 final size:3
Alignment explanation
Indices: 1971716--1971759 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
1971706 ATTATTTATT
*
1971716 TAA TAA TAA TAA TAA TAA TAA TAA TAA TATT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA T
1971760 CATTTTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 36 0.95
4 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1972011 original size:44 final size:45
Alignment explanation
Indices: 1971949--1972082 Score: 171
Period size: 45 Copynumber: 3.0 Consensus size: 45
1971939 CTTATCATCT
* * *
1971949 TGCACTGTAGGTCTTACAGATGACCCGGAGGATTTGAAAA-ATCA
1 TGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAATATCA
* * * * *
1971993 TGTACTGAGGGGCTTACAGATGATCCGAAGGCTTTAAAAATATCA
1 TGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAATATCA
* *
1972038 TGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAAAATATCA
1 TGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAATATCA
1972083 AAAAGCTCCC
Statistics
Matches: 75, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
44 32 0.43
45 43 0.57
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (45 bp):
TGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAATATCA
Found at i:1972162 original size:45 final size:45
Alignment explanation
Indices: 1972090--1972450 Score: 587
Period size: 45 Copynumber: 8.0 Consensus size: 45
1972080 TCAAAAAGCT
*
1972090 CCCGAAGGCTTTTTGAAAACATTATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* *
1972137 TCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTATAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1972182 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1972227 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
1972272 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGG
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
1972317 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTATAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* **
1972362 CCCAAAGGTTTTGAAAACATCATAAACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* * * * *
1972407 CCCAAAGGTTTTGAAATCATCATGCATTGTAGGTCTTACAGATG
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
1972451 TGGGAAATAG
Statistics
Matches: 296, Mismatches: 18, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
45 289 0.98
47 7 0.02
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.25
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:1973718 original size:122 final size:122
Alignment explanation
Indices: 1973501--1973865 Score: 606
Period size: 122 Copynumber: 3.0 Consensus size: 122
1973491 GACATTAGCC
* *
1973501 TTCATTGGACTAATTAAACAGTTCAACTCATCATAATGTCTTTGACTTGACAATCACAGTGGAGT
1 TTCATTGGACTAATTAAACAGTTCAACTCATCACAATGTCTTTGACTTGACAATCACAGTGGAGC
1973566 AAACACCGAACTGCCAAATATCCGATCAAGGTCATGCTTTGAATATATGACTTTTTT
66 AAACACCGAACTGCCAAATATCCGATCAAGGTCATGCTTTGAATATATGACTTTTTT
* *
1973623 TTCATTAGACTAATTAAACAGTTCAACTCATCACAATATCTTTGACTTGACAATCACAGTGGAGC
1 TTCATTGGACTAATTAAACAGTTCAACTCATCACAATGTCTTTGACTTGACAATCACAGTGGAGC
* *
1973688 AAACGCCGAACTGCCAAATACCCGATCAAGGTCATGCTTTGAATATATGACTTTTTT
66 AAACACCGAACTGCCAAATATCCGATCAAGGTCATGCTTTGAATATATGACTTTTTT
* ** *
1973745 TTCATTGGACTAACTAAAGTGTTCAACTCATAACAATGTCTTTGACTTGACAATCACAGTGGAGC
1 TTCATTGGACTAATTAAACAGTTCAACTCATCACAATGTCTTTGACTTGACAATCACAGTGGAGC
* * *
1973810 AAACATCGAACTGCCAAATATCCGATCAAGATCATGTTTTGAATATATGA-TTTTTT
66 AAACACCGAACTGCCAAATATCCGATCAAGGTCATGCTTTGAATATATGACTTTTTT
1973866 ATAAGAACTT
Statistics
Matches: 226, Mismatches: 17, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
121 6 0.03
122 220 0.97
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (122 bp):
TTCATTGGACTAATTAAACAGTTCAACTCATCACAATGTCTTTGACTTGACAATCACAGTGGAGC
AAACACCGAACTGCCAAATATCCGATCAAGGTCATGCTTTGAATATATGACTTTTTT
Found at i:1980220 original size:32 final size:32
Alignment explanation
Indices: 1980147--1980222 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
1980137 ACTGGGACTT
* * *
1980147 GACCCGACTCGAATATCACACTTAAAAAAACT
1 GACCTGACCCGAATATCACACTTAAAAAAACC
* *
1980179 GA-CTCGACCCGAATATCACACTTAAAACACCC
1 GACCT-GACCCGAATATCACACTTAAAAAAACC
1980211 GACCTGACCCGA
1 GACCTGACCCGA
1980223 CCTGAATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 1 0.03
32 34 0.92
33 2 0.05
ACGTcount: A:0.38, C:0.34, G:0.12, T:0.16
Consensus pattern (32 bp):
GACCTGACCCGAATATCACACTTAAAAAAACC
Found at i:1980458 original size:5 final size:5
Alignment explanation
Indices: 1980448--1980473 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1980438 AAAAAAATCA
1980448 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
1980474 ATATATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:1980762 original size:24 final size:24
Alignment explanation
Indices: 1980735--1980786 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
1980725 CCAAATCCCC
1980735 CCAATTCCAAGGGATTCCATCCAA
1 CCAATTCCAAGGGATTCCATCCAA
* *
1980759 CCAATTCCAAGGGATTTCATTCAA
1 CCAATTCCAAGGGATTCCATCCAA
1980783 CCAA
1 CCAA
1980787 ACGCCACCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.31, G:0.12, T:0.23
Consensus pattern (24 bp):
CCAATTCCAAGGGATTCCATCCAA
Found at i:1981077 original size:20 final size:20
Alignment explanation
Indices: 1981052--1981102 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1981042 AAGTGAAGTT
*
1981052 TGGTGAGTCACCAAACTATG
1 TGGTGACTCACCAAACTATG
1981072 TGGTGACTCACCAAACTATG
1 TGGTGACTCACCAAACTATG
1981092 TGGTGACTCAC
1 TGGTGACTCAC
1981103 AATAGAGTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (20 bp):
TGGTGACTCACCAAACTATG
Found at i:1981355 original size:3 final size:3
Alignment explanation
Indices: 1981347--1981421 Score: 105
Period size: 3 Copynumber: 24.3 Consensus size: 3
1981337 ATTATTTATT
* *
1981347 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGTA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
*
1981393 TAA TAA TATT TAA TAA TAA TAA TAA TAA T
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA T
1981422 TTTAAAAATA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
3 60 0.94
4 4 0.06
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1981387 original size:25 final size:25
Alignment explanation
Indices: 1981347--1981421 Score: 116
Period size: 25 Copynumber: 3.0 Consensus size: 25
1981337 ATTATTTATT
1981347 TAATA-ATAATAATAATAATAATAA
1 TAATATATAATAATAATAATAATAA
* *
1981371 TAATGTATAATATTAATAATAATAA
1 TAATATATAATAATAATAATAATAA
*
1981396 TAATATTTAATAATAATAATAATAA
1 TAATATATAATAATAATAATAATAA
1981421 T
1 T
1981422 TTTAAAAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
24 4 0.09
25 41 0.91
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (25 bp):
TAATATATAATAATAATAATAATAA
Found at i:1982182 original size:392 final size:392
Alignment explanation
Indices: 1981456--1982252 Score: 1172
Period size: 392 Copynumber: 2.0 Consensus size: 392
1981446 AGTGTTTACA
* *
1981456 AATACCACTAAAGTAATCGTGTTCTCACAGCCCATGTAAACGTTCCAGATACGGTTAACCGGTAA
1 AATACCACTAAAGTAATCGTGTTCTCACAGCCCATCTAAACGTTCCAGATAAGGTTAACCGGTAA
* * *
1981521 AAGGTGAGTCTCACATTATAAAAGCTCTTTTCGCCATGTTTAGCCAGTATAATCCTTGACTAAAT
66 AAAGTGAGTCTCACATTATAAAAGCTCTTTTCACCATGTTTAGCCAGTAAAATCCTTGACTAAAT
* * *
1981586 AAGCTAACAGGCACCTTCTACGAACTCTTACAAGCAAAATGTACCACTTTGGTTCACAATTTAAT
131 AAGCTAACAGACACCTTCTACGAACTCTTACAAGCAAAATGTACCACTTTGGTTCACAAATTAAG
* *
1981651 ATCTATTAGACAAAAAGTCGACTGTTTCAACAAAAGAAAAACCAATTAAATGCCGAAAAATGATT
196 ATCTATTAGACAAAAAGTCGACTGTTTCAACAAAAGAAAAACCAATTAAACGCCGAAAAACGATT
* * *
1981716 GTTCTGTAGCTACTACTAATGTTAACAGATGCAAAACTAAAATGAAATATAGGAGATTCAACAAC
261 GCTCTGCAGCTACTACTAAAGTTAACAGATGCAAAACTAAAATGAAATATAGGAGATTCAACAAC
*
1981781 ACCTTCTTATAGCAGATTCAACTAATGAATGAA-TTAAACTC-TCCTTGGCTAATCAAAACTTAC
326 ACCTTCTTATAGAAGATTCAACTAATGAATGAATTTAAACTCGTCCTTGGCTAATC-AAACTTAC
*
1981844 TGC
390 TAC
* * * *
1981847 AATACCACTAAAGTAATCGTGTTCTCACGGTCCATCTGAAACGTTCCAGATAATGTTAACTGGTA
1 AATACCACTAAAGTAATCGTGTTCTCACAGCCCATCT-AAACGTTCCAGATAAGGTTAACCGGTA
* * *
1981912 AAAAGTGAGTTTCACATTATAAAAGGTCTTTTCACCATGTTTAGCTA-TCAAAATCCTTGACTAA
65 AAAAGTGAGTCTCACATTATAAAAGCTCTTTTCACCATGTTTAGCCAGT-AAAATCCTTGACTAA
** * * *
1981976 ATAAGCTAACAGATTCCTTCTATGAACTCTTACATGCAAAATGTACCACTTTGGTTCGCAAATTA
129 ATAAGCTAACAGACACCTTCTACGAACTCTTACAAGCAAAATGTACCACTTTGGTTCACAAATTA
* * * *
1982041 AGATCTATTCGACAAAAAGTCGACTGTTTCGACAAAAGAAAAATCGATTAAACGCCCG-AAAACG
194 AGATCTATTAGACAAAAAGTCGACTGTTTCAACAAAAGAAAAACCAATTAAACG-CCGAAAAACG
* * *
1982105 ATTGCTCTGCAGTTACTTCTAAAG-TAACAGATGCAAAACTAGAATGAAATATAGGAGATTCAAC
258 ATTGCTCTGCAGCTACTACTAAAGTTAACAGATGCAAAACTAAAATGAAATATAGGAGATTCAAC
* *
1982169 AATACCTTTCTTATAGAAGATTCAACTAATGAATGAATTTAAACTCGGTCCTTTGCTAATCAAAC
323 AACACC-TTCTTATAGAAGATTCAACTAATGAATGAATTTAAACTC-GTCCTTGGCTAATCAAAC
*
1982234 TTACTAT
386 TTACTAC
1982241 AATACCACTAAA
1 AATACCACTAAA
1982253 TCATTTACAG
Statistics
Matches: 362, Mismatches: 37, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
391 79 0.22
392 239 0.66
393 11 0.03
394 21 0.06
395 12 0.03
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.29
Consensus pattern (392 bp):
AATACCACTAAAGTAATCGTGTTCTCACAGCCCATCTAAACGTTCCAGATAAGGTTAACCGGTAA
AAAGTGAGTCTCACATTATAAAAGCTCTTTTCACCATGTTTAGCCAGTAAAATCCTTGACTAAAT
AAGCTAACAGACACCTTCTACGAACTCTTACAAGCAAAATGTACCACTTTGGTTCACAAATTAAG
ATCTATTAGACAAAAAGTCGACTGTTTCAACAAAAGAAAAACCAATTAAACGCCGAAAAACGATT
GCTCTGCAGCTACTACTAAAGTTAACAGATGCAAAACTAAAATGAAATATAGGAGATTCAACAAC
ACCTTCTTATAGAAGATTCAACTAATGAATGAATTTAAACTCGTCCTTGGCTAATCAAACTTACT
AC
Found at i:1990826 original size:59 final size:58
Alignment explanation
Indices: 1990725--1990842 Score: 134
Period size: 59 Copynumber: 2.0 Consensus size: 58
1990715 GACCATTTTT
* * **
1990725 TAACTTTTAATAGTTGAGGGACTTAATAAAGCAACATCCTATAGTTGGAGGATCATTTA
1 TAACTTTTAATAGTAGAGGGACTTAACAAAGCAACATCCTATAG-ACGAGGATCATTTA
*
1990784 TAACTTTTAATAGTCAGA-GGACTTAACAAA-TAA-ATGCTCTATAGACGAGGATCATTTA
1 TAACTTTTAATAGT-AGAGGGACTTAACAAAGCAACAT-C-CTATAGACGAGGATCATTTA
1990842 T
1 T
1990843 GTACTTTACC
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
57 2 0.04
58 16 0.31
59 31 0.61
60 2 0.04
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (58 bp):
TAACTTTTAATAGTAGAGGGACTTAACAAAGCAACATCCTATAGACGAGGATCATTTA
Found at i:1993854 original size:7 final size:7
Alignment explanation
Indices: 1993842--1994084 Score: 149
Period size: 7 Copynumber: 32.7 Consensus size: 7
1993832 TCTGAGATAA
1993842 TATATAT
1 TATATAT
1993849 TATATAT
1 TATATAT
*
1993856 TATAGTAG
1 TATA-TAT
1993864 TATATAT
1 TATATAT
1993871 TATATAT
1 TATATAT
1993878 ACCATATATAT
1 ----TATATAT
* *
1993889 TATAAAA
1 TATATAT
1993896 TATATAT
1 TATATAT
*
1993903 TATATGTAA
1 TATA--TAT
* *
1993912 TGTATAA
1 TATATAT
1993919 TATATAT
1 TATATAT
1993926 TATACATAT
1 TAT--ATAT
1993935 T-TATAT
1 TATATAT
*
1993941 TATATAG
1 TATATAT
1993948 TATATAT
1 TATATAT
1993955 TAAAGTATAT
1 T--A-TATAT
*
1993965 TATTATAC
1 TA-TATAT
1993973 T-TATAT
1 TATATAT
1993979 TATATAT
1 TATATAT
1993986 TATATA-
1 TATATAT
1993992 T-TATAT
1 TATATAT
1993998 TATATTAT
1 TATA-TAT
1994006 TATTATTAT
1 TA-TA-TAT
*
1994015 AATATAT
1 TATATAT
1994022 TAGTCATTAT
1 TA-T-A-TAT
1994032 TATAT-T
1 TATATAT
*
1994038 CTATTTAT
1 -TATATAT
1994046 TATATAT
1 TATATAT
1994053 TATATAT
1 TATATAT
*
1994060 TATATAC
1 TATATAT
1994067 TAT-TAT
1 TATATAT
1994073 T-TATTAT
1 TATA-TAT
1994080 TATAT
1 TATAT
1994085 TAATATTATT
Statistics
Matches: 189, Mismatches: 21, Indels: 52
0.72 0.08 0.20
Matches are distributed among these distances:
5 5 0.03
6 16 0.08
7 105 0.56
8 25 0.13
9 20 0.11
10 11 0.06
11 7 0.04
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (7 bp):
TATATAT
Found at i:1993859 original size:5 final size:5
Alignment explanation
Indices: 1993851--1994093 Score: 105
Period size: 5 Copynumber: 49.6 Consensus size: 5
1993841 ATATATATTA
* * * * *
1993851 TATAT TATAG TAGTA- TATAT TATA- TATAC CATA- TATAT TATAA AATA-
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
*
1993898 TATAT TATAT GTA-AT GTATAAT ATATAT TATA- CATATT TATAT TATA-
1 TATAT TATAT -TATAT -TAT-AT -TATAT TATAT TATA-T TATAT TATAT
* *
1993945 TAGTA- TATAT TAAAG TATA- T-TAT TATACT TATAT TATA- TAT-T ATATAT
1 TA-TAT TATAT TATAT TATAT TATAT TATA-T TATAT TATAT TATAT -TATAT
*
1993993 TATAT TATA- T-TAT TATTAT TATAA TATAT TAGTCA- T-TAT TATAT
1 TATAT TATAT TATAT TA-TAT TATAT TATAT TA-T-AT TATAT TATAT
*
1994037 TCTAT T-TAT TATA- TAT-T ATATAT TATA- TACTAT TAT-T TATTAT
1 TATAT TATAT TATAT TATAT -TATAT TATAT TA-TAT TATAT TA-TAT
1994080 TATAT TAATAT TAT
1 TATAT T-ATAT TAT
1994094 TTTTTCGGTT
Statistics
Matches: 189, Mismatches: 15, Indels: 68
0.69 0.06 0.25
Matches are distributed among these distances:
3 5 0.03
4 40 0.21
5 105 0.56
6 33 0.17
7 6 0.03
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (5 bp):
TATAT
Found at i:1993970 original size:3 final size:3
Alignment explanation
Indices: 1993962--1994094 Score: 82
Period size: 3 Copynumber: 43.3 Consensus size: 3
1993952 TATTAAAGTA
1993962 TAT TAT TA- TACT TA- TAT TAT ATAT TAT ATAT TA- TAT TA- TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT -TAT TAT -TAT TAT TAT TAT TAT TAT
* * *
1994006 TAT TAT TAT AAT ATAT TAGT CAT TAT TA- TAT T-C TATT TAT TAT ATAT
1 TAT TAT TAT TAT -TAT TA-T TAT TAT TAT TAT TAT TA-T TAT TAT -TAT
* *
1994053 TAT ATAT TAT ATAC TAT TATT TAT TAT TA- TAT TAA TAT TAT T
1 TAT -TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
1994095 TTTTCGGTTT
Statistics
Matches: 103, Mismatches: 10, Indels: 34
0.70 0.07 0.23
Matches are distributed among these distances:
2 13 0.13
3 65 0.63
4 25 0.24
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:1993977 original size:38 final size:37
Alignment explanation
Indices: 1993921--1994093 Score: 122
Period size: 38 Copynumber: 4.6 Consensus size: 37
1993911 ATGTATAATA
*
1993921 TATATTATACATATTTATATTATATAGTATATATTAAAG
1 TATATTAT-TATA-TTATATTATATAGTATATATTAAAG
* * *
1993960 TATATTATTATACTTATATTATATATTATATATTATAT
1 TATATTATTATA-TTATATTATATAGTATATATTAAAG
* * *
1993998 TATATTATTATTATTATAATATATTAGTCAT-TATTATAT
1 TATATTATTA-TATTATATTATA-TAGT-ATATATTAAAG
* * * *
1994037 TCTA-T-TTAT-TATATATTATATATTATATACTATTA-
1 TATATTATTATAT-TATATTATATAGTATATATTA-AAG
*
1994072 TTTATTATTATATTAATATTAT
1 TATATTATTATATT-ATATTAT
1994094 TTTTTCGGTT
Statistics
Matches: 112, Mismatches: 12, Indels: 21
0.77 0.08 0.14
Matches are distributed among these distances:
34 2 0.02
35 11 0.10
36 12 0.11
37 8 0.07
38 53 0.47
39 24 0.21
40 2 0.02
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (37 bp):
TATATTATTATATTATATTATATAGTATATATTAAAG
Found at i:1994049 original size:48 final size:49
Alignment explanation
Indices: 1993990--1994085 Score: 135
Period size: 48 Copynumber: 2.0 Consensus size: 49
1993980 ATATATTATA
1993990 TATTATATTATATTATTAT-TATTATAATA-TATTAGTCATTATTATATTC
1 TATTATATTATA-TATTATATATTAT-ATACTATTAGTCATTATTATATTC
* *
1994039 TATT-TATTATATATTATATATTATATACTATTATTTATTATTATATT
1 TATTATATTATATATTATATATTATATACTATTAGTCATTATTATATT
1994086 AATATTATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
47 9 0.21
48 30 0.70
49 4 0.09
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.59
Consensus pattern (49 bp):
TATTATATTATATATTATATATTATATACTATTAGTCATTATTATATTC
Found at i:2002101 original size:21 final size:21
Alignment explanation
Indices: 2002079--2002217 Score: 152
Period size: 21 Copynumber: 6.5 Consensus size: 21
2002069 TACGCCGTCA
* *
2002079 TTCGGGACATATATGTGGTCA
1 TTCGGGACATTTATGTGGTCC
* * * *
2002100 TTTGGAACATATATGTGGTCA
1 TTCGGGACATTTATGTGGTCC
* *
2002121 TTCGGGACGGTTTTACGTGGTCC
1 TTCGGGAC--ATTTATGTGGTCC
*
2002144 TTCAGGACATTTATGTGGTCC
1 TTCGGGACATTTATGTGGTCC
*
2002165 TTCGGGACATTTATGTGATCC
1 TTCGGGACATTTATGTGGTCC
* *
2002186 TTTGGGACATTTATGCGGTCC
1 TTCGGGACATTTATGTGGTCC
2002207 TTCGGGACATT
1 TTCGGGACATT
2002218 CTATATGGCA
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
21 83 0.84
23 16 0.16
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (21 bp):
TTCGGGACATTTATGTGGTCC
Found at i:2006415 original size:20 final size:20
Alignment explanation
Indices: 2006386--2006423 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2006376 CCTGTGGGGG
*
2006386 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
2006406 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
2006424 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:2020040 original size:5 final size:5
Alignment explanation
Indices: 2020032--2020248 Score: 98
Period size: 5 Copynumber: 43.0 Consensus size: 5
2020022 CGGGATATTA
* *
2020032 TATAT TATAT AGTAGTAT TATAT TATA- TATAT CATATAT TATAA AATA-
1 TATAT TATAT --TA-TAT TATAT TATAT TATAT --TATAT TATAT TATAT
* * * *
2020080 TATAT TATAT AATA- CATAT TATAG TA-AT ATATAT TATA- CATATT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT -TATAT TATAT TATA-T TATAT
* * *
2020129 TATAT AATA- TATAT TAAAG TATA- -ATAT TATACT TATATT ATATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATA-T TATA-T -TATAT
* * *
2020174 TATAG TATATT GTAGAT TATAT TATTAT TATA- -GTAT TATAT TATAT
1 TATAT TATA-T -TATAT TATAT TA-TAT TATAT TATAT TATAT TATAT
* *
2020220 TA-GT TATAGT TACAT TATAT T-TAT TATAT
1 TATAT TATA-T TATAT TATAT TATAT TATAT
2020249 ATTACATACT
Statistics
Matches: 161, Mismatches: 26, Indels: 50
0.68 0.11 0.21
Matches are distributed among these distances:
3 5 0.03
4 24 0.15
5 91 0.57
6 24 0.15
7 14 0.09
8 3 0.02
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (5 bp):
TATAT
Found at i:2020042 original size:2 final size:2
Alignment explanation
Indices: 2020026--2020183 Score: 75
Period size: 2 Copynumber: 85.0 Consensus size: 2
2020016 TGCGTTCGGG
2020026 AT AT -T AT AT AT -T AT AT AGT AGT AT -T AT AT -T AT AT AT AT CAT
1 AT AT AT AT AT AT AT AT AT A-T A-T AT AT AT AT AT AT AT AT AT -AT
* *
2020067 AT AT -T AT A- AA AT AT AT AT -T AT AT A- AT AC AT AT -T AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* *
2020105 A- AT AT AT AT -T AT AC AT AT TT AT AT -T AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2020143 -T AA AGT AT A- AT AT -T AT ACT -T AT AT -T AT AT AT -T AT AGT
1 AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T
2020180 AT AT
1 AT AT
2020184 TGTAGATTAT
Statistics
Matches: 122, Mismatches: 9, Indels: 50
0.67 0.05 0.28
Matches are distributed among these distances:
1 19 0.16
2 90 0.74
3 13 0.11
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2020068 original size:9 final size:8
Alignment explanation
Indices: 2020026--2020183 Score: 75
Period size: 7 Copynumber: 21.2 Consensus size: 8
2020016 TGCGTTCGGG
2020026 ATAT-TAT
1 ATATATAT
2020033 ATAT-TAT
1 ATATATAT
2020040 ATAGTAGTAT
1 ATA-TA-TAT
2020050 -TATAT-T
1 ATATATAT
2020056 ATATATAT
1 ATATATAT
2020064 CATATAT-T
1 -ATATATAT
*
2020072 ATA-AAAT
1 ATATATAT
2020079 ATATAT-T
1 ATATATAT
2020086 ATATA-AT
1 ATATATAT
*
2020093 ACATAT-T
1 ATATATAT
2020100 ATAGTA-AT
1 ATA-TATAT
2020108 ATATAT-T
1 ATATATAT
*
2020115 ATACATAT
1 ATATATAT
*
2020123 TTATAT-T
1 ATATATAT
2020130 ATATA-AT
1 ATATATAT
2020137 ATATAT-T
1 ATATATAT
*
2020144 AAAGTATA-
1 ATA-TATAT
2020152 ATAT-TAT
1 ATATATAT
2020159 ACT-TATAT
1 A-TATATAT
2020167 -TATATAT
1 ATATATAT
2020174 -TATAGTAT
1 ATATA-TAT
2020182 AT
1 AT
2020184 TGTAGATTAT
Statistics
Matches: 117, Mismatches: 10, Indels: 46
0.68 0.06 0.27
Matches are distributed among these distances:
6 5 0.04
7 71 0.61
8 29 0.25
9 9 0.08
10 3 0.03
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (8 bp):
ATATATAT
Found at i:2020118 original size:24 final size:23
Alignment explanation
Indices: 2020051--2020177 Score: 83
Period size: 24 Copynumber: 5.7 Consensus size: 23
2020041 TAGTAGTATT
* *
2020051 ATATTATA-TATATCATATATTAT
1 ATATTATAGTATAT-ATATAATAC
* *
2020074 AAAATATA-TAT-TATATAATAC
1 ATATTATAGTATATATATAATAC
*
2020095 ATATTATAGTAATATATATTATAC
1 ATATTATAGT-ATATATATAATAC
*
2020119 ATATT-TA-TAT-TATATAATAT
1 ATATTATAGTATATATATAATAC
* *
2020139 ATATTAAAGTATA-ATATTATAC
1 ATATTATAGTATATATATAATAC
2020161 TTATATTATA-TAT-TATA
1 --ATATTATAGTATATATA
2020178 GTATATTGTA
Statistics
Matches: 82, Mismatches: 13, Indels: 18
0.73 0.12 0.16
Matches are distributed among these distances:
20 13 0.16
21 16 0.20
22 13 0.16
23 19 0.23
24 21 0.26
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATTATAGTATATATATAATAC
Found at i:2020128 original size:44 final size:44
Alignment explanation
Indices: 2020051--2020177 Score: 145
Period size: 44 Copynumber: 2.9 Consensus size: 44
2020041 TAGTAGTATT
* *
2020051 ATATTATA-TATATCATATATTATA-AAATATATATTATATAATAC
1 ATATTATAGTA-AT-ATATATTATACATATTTATATTATATAATAC
*
2020095 ATATTATAGTAATATATATTATACATATTTATATTATATAATAT
1 ATATTATAGTAATATATATTATACATATTTATATTATATAATAC
*
2020139 ATATTAAAGT-ATA-ATATTATACTTATATTATATATTATA
1 ATATTATAGTAATATATATTATAC--ATATT-TATATTATA
2020178 GTATATTGTA
Statistics
Matches: 74, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
42 9 0.12
43 13 0.18
44 41 0.55
45 11 0.15
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (44 bp):
ATATTATAGTAATATATATTATACATATTTATATTATATAATAC
Found at i:2020171 original size:31 final size:29
Alignment explanation
Indices: 2020030--2020221 Score: 134
Period size: 29 Copynumber: 6.5 Consensus size: 29
2020020 TTCGGGATAT
*
2020030 TATATATTATA-TAGTAGTATTATATTATA-
1 TATATATTATATTA-TATTA-TATATTATAG
*
2020059 TATATCA-TATATTATAAAATATATATTATA-
1 TATAT-ATTATATTAT--ATTATATATTATAG
*
2020089 TA-ATA-CATATTATAGTAATATATATTATA-
1 TATATATTATATTATA-T--TATATATTATAG
* *
2020118 CATAT-TTATATTATATAATATATATTAAAG
1 TATATATTATATTATAT--TATATATTATAG
2020148 TATAATATTATACTTATATTATATATTATAG
1 TAT-ATATTATA-TTATATTATATATTATAG
*
2020179 TATAT-TGTAGATTATATTAT-TATTATAG
1 TATATAT-TATATTATATTATATATTATAG
2020207 TATTATATTATATTA
1 TA-TATATTATATTA
2020222 GTTATAGTTA
Statistics
Matches: 137, Mismatches: 10, Indels: 32
0.77 0.06 0.18
Matches are distributed among these distances:
26 1 0.01
28 18 0.13
29 56 0.41
30 32 0.23
31 19 0.14
32 5 0.04
33 6 0.04
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (29 bp):
TATATATTATATTATATTATATATTATAG
Found at i:2020246 original size:20 final size:20
Alignment explanation
Indices: 2020198--2020270 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 20
2020188 GATTATATTA
*
2020198 TTATTATAGTATTATATTATA-
1 TTATTATAG--TTACATTATAT
2020219 TTAGTTATAGTTACATTATAT
1 TTA-TTATAGTTACATTATAT
*
2020240 TTATTATATATTACATACTACTAT
1 TTATTATA-GTTACAT--TA-TAT
2020264 TTATTAT
1 TTATTAT
2020271 TATATTGATA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
20 14 0.32
21 12 0.27
22 6 0.14
23 2 0.05
24 10 0.23
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (20 bp):
TTATTATAGTTACATTATAT
Found at i:2023302 original size:77 final size:79
Alignment explanation
Indices: 2023197--2023351 Score: 203
Period size: 77 Copynumber: 2.0 Consensus size: 79
2023187 TTTGAATTAA
*
2023197 TTAAAATCTTATTTAATTAATTCAAATTAAATAT-TCATT-AAAG-GCTTATAATTCGAATTACA
1 TTAAAATCTTATTTAATTAATTCAAATTAAATATCT-ATTAAAAGAG-TTATAATTAGAATTACA
2023259 TTC-TTTAACGTTTAT
64 TTCTTTTAACGTTTAT
* * *
2023274 TTAAACTCTTATTTAATT-ATTCCGAATTAAGTATCTATTAAAAGAGTTATAATTAGAATTACAT
1 TTAAAATCTTATTTAATTAATT-CAAATTAAATATCTATTAAAAGAGTTATAATTAGAATTACAT
*
2023338 TCTTTTAATGTTTA
65 TCTTTTAACGTTTA
2023352 CTTACTATAT
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
76 3 0.04
77 30 0.44
78 24 0.35
79 11 0.16
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (79 bp):
TTAAAATCTTATTTAATTAATTCAAATTAAATATCTATTAAAAGAGTTATAATTAGAATTACATT
CTTTTAACGTTTAT
Found at i:2031052 original size:21 final size:21
Alignment explanation
Indices: 2031026--2031065 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2031016 TTATATGTGA
*
2031026 TATGTGGTCCTTCGGGACATC
1 TATGTGGTCATTCGGGACATC
*
2031047 TATGTGGTTATTCGGGACA
1 TATGTGGTCATTCGGGACA
2031066 AATTCATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.30, T:0.35
Consensus pattern (21 bp):
TATGTGGTCATTCGGGACATC
Done.