Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000913.1 Hibiscus syriacus cultivar Beakdansim tig00001818_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: 1610646
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:912897 original size:17 final size:17
Alignment explanation
Indices: 912875--912932 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
912865 AATAATAACA
*
912875 TAATATTTTTCAATTTT
1 TAATATTTATCAATTTT
* *
912892 TAATATTTATAAATATT
1 TAATATTTATCAATTTT
* *
912909 AAATATTTGA-CAAATTT
1 TAATATTT-ATCAATTTT
912926 TAATATT
1 TAATATT
912933 ATATATAATT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
17 31 0.97
18 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.53
Consensus pattern (17 bp):
TAATATTTATCAATTTT
Found at i:913955 original size:20 final size:19
Alignment explanation
Indices: 913927--913986 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 19
913917 TACTTTAAAG
913927 ATTAAAATTTTATAAATAAT
1 ATTAAAA-TTTATAAATAAT
*
913947 ATTATAATTTATAAAT-AT
1 ATTAAAATTTATAAATAAT
* * *
913965 -TAAAAAATTATAATTAAT
1 ATTAAAATTTATAAATAAT
913983 ATTA
1 ATTA
913987 TAAGCATAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
17 11 0.34
18 4 0.12
19 11 0.34
20 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTAAAATTTATAAATAAT
Found at i:916459 original size:20 final size:22
Alignment explanation
Indices: 916408--916460 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
916398 AATGTACACT
* *
916408 AGTATCGATACTAAGCCTTTCG
1 AGTATCGATACTAACCCCTTCG
*
916430 -GTATCAATACT-ACCCCTT-G
1 AGTATCGATACTAACCCCTTCG
916449 AGTATCGATACT
1 AGTATCGATACT
916461 CCTCTCAGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.04
20 15 0.58
21 10 0.38
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (22 bp):
AGTATCGATACTAACCCCTTCG
Found at i:923704 original size:12 final size:12
Alignment explanation
Indices: 923689--923728 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
923679 ATATATATAT
923689 AATTTAATTTAA
1 AATTTAATTTAA
* *
923701 AATTTACTTTAT
1 AATTTAATTTAA
923713 AATTTAATTTAA
1 AATTTAATTTAA
923725 AATT
1 AATT
923729 AACTATAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTAATTTAA
Found at i:926252 original size:14 final size:14
Alignment explanation
Indices: 926233--926291 Score: 100
Period size: 14 Copynumber: 4.2 Consensus size: 14
926223 GAGAGAGAAG
926233 GAGGCGCATGATAA
1 GAGGCGCATGATAA
926247 GAGGCGCATGATAA
1 GAGGCGCATGATAA
926261 GAGGCGCATGATAA
1 GAGGCGCATGATAA
* *
926275 GAGGTGCATGAAAA
1 GAGGCGCATGATAA
926289 GAG
1 GAG
926292 ACGCGCCTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 43 1.00
ACGTcount: A:0.37, C:0.12, G:0.37, T:0.14
Consensus pattern (14 bp):
GAGGCGCATGATAA
Found at i:929861 original size:83 final size:82
Alignment explanation
Indices: 929763--930194 Score: 403
Period size: 83 Copynumber: 5.2 Consensus size: 82
929753 TCCTCTGAAT
* * * **
929763 AATATATAATGGAAAATGCTTCCCCTAGAACGCTCATTTCATTTTAGATGGGATTAAACACTATG
1 AATA-ATAATGGAAAACGCTTCCCCTGGAACGCTC-TTTCATTTTCGATGGGATGGAACACTATG
* * *
929828 ATATGGAAGAAATTCTTTG
64 ACATGGAAGAGATTCTCTG
* * * ** * *
929847 AATAATAATGGAAAATGATTACTTTGGAATGCGC-CTTTCA-TTTCGGATGTGATTGAACACTAT
1 AATAATAATGGAAAACGCTTCCCCTGGAA--CGCTCTTTCATTTTC-GATGGGATGGAACACTAT
*
929910 GACAT-GACAGAGATTCTATG
63 GACATGGA-AGAGATTCTCTG
* * * * * *
929930 AATAAAAATGGAAAACGCTTCCCTTGAAATGCTTCTTTCA-TTTCGAAAGAGATGGAACACTATG
1 AATAATAATGGAAAACGCTTCCCCTGGAACGC-TCTTTCATTTTCG-ATGGGATGGAACACTATG
*
929994 ACATGGCAGAGATTCTCTG
64 ACATGGAAGAGATTCTCTG
* * * *
930013 GATAATAATGGAAAACACTTCCCTTGGAACGTGTCTTTCA-TTTCGAATGGGATGGAACACTATG
1 AATAATAATGGAAAACGCTTCCCCTGGAACG-CTCTTTCATTTTCG-ATGGGATGGAACACTATG
*
930077 ACATGGCAGAGATTCTCTG
64 ACATGGAAGAGATTCTCTG
* *
930096 AATAATAATGAAAAACGCTTCCCCTGGAAAGCGC-CTTTCA-TTTCGGATGGGATGAAACACTAT
1 AATAATAATGGAAAACGCTTCCCCTGG-AA-CGCTCTTTCATTTTC-GATGGGATGGAACACTAT
*
930159 GACAT-GACAGAGATTCTCTA
63 GACATGGA-AGAGATTCTCTG
930179 AATAATAATGGAAAAC
1 AATAATAATGGAAAAC
930195 ATTATGACAT
Statistics
Matches: 295, Mismatches: 40, Indels: 27
0.81 0.11 0.07
Matches are distributed among these distances:
81 2 0.01
82 7 0.02
83 272 0.92
84 9 0.03
85 5 0.02
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (82 bp):
AATAATAATGGAAAACGCTTCCCCTGGAACGCTCTTTCATTTTCGATGGGATGGAACACTATGAC
ATGGAAGAGATTCTCTG
Found at i:930020 original size:166 final size:166
Alignment explanation
Indices: 929818--930195 Score: 481
Period size: 166 Copynumber: 2.3 Consensus size: 166
929808 AGATGGGATT
* * * * * * *
929818 AAACACTATGATATGGAAGAAATTCTTTGAATAATAATGGAAAATGA-TTACTTTGGAATGCGCC
1 AAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAAAA-CACTTACCTTGGAACGCGCC
* * * *
929882 TTTCATTTCGGATGTGATTGAACACTATGACATGACAGAGATTCTATGAATAAAAATGGAAAACG
65 TTTCATTTCGAATGGGATGGAACACTATGACATGACAGAGATTCTATGAATAAAAATGAAAAACG
* **
929947 CTT-CCCTTGAAATGCTTCTTTCATTTCGAAAGAGATG
130 CTTCCCCTGGAAA-GCGCCTTTCATTTCGAAAGAGATG
* * * * *
929984 GAACACTATGACATGGCAGAGATTCTCTGGATAATAATGGAAAACACTTCCCTTGGAACGTGTCT
1 AAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAAAACACTTACCTTGGAACGCGCCT
* * *
930049 TTCATTTCGAATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGAAAAACGC
66 TTCATTTCGAATGGGATGGAACACTATGACATGACAGAGATTCTATGAATAAAAATGAAAAACGC
* * *
930114 TTCCCCTGGAAAGCGCCTTTCATTTCGGATGGGATG
131 TTCCCCTGGAAAGCGCCTTTCATTTCGAAAGAGATG
* *
930150 AAACACTATGACATGACAGAGATTCTCTAAATAATAATGGAAAACA
1 AAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAAAACA
930196 TTATGACATG
Statistics
Matches: 181, Mismatches: 29, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
165 1 0.01
166 172 0.95
167 8 0.04
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28
Consensus pattern (166 bp):
AAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAAAACACTTACCTTGGAACGCGCCT
TTCATTTCGAATGGGATGGAACACTATGACATGACAGAGATTCTATGAATAAAAATGAAAAACGC
TTCCCCTGGAAAGCGCCTTTCATTTCGAAAGAGATG
Found at i:931102 original size:26 final size:27
Alignment explanation
Indices: 931073--931124 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
931063 TGAACTATAA
*
931073 AAACAACAAACTA-TAAACATTACATT
1 AAACAACAAACTATTAAACATGACATT
931099 AAACAACAAACTATTAAACATGACAT
1 AAACAACAAACTATTAAACATGACAT
931125 AAAGCATACC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.58, C:0.19, G:0.02, T:0.21
Consensus pattern (27 bp):
AAACAACAAACTATTAAACATGACATT
Found at i:931217 original size:32 final size:32
Alignment explanation
Indices: 931172--931246 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 32
931162 TATTTCACAG
* *
931172 ACCTTAAATAGTAAATAAAAGCATACACATAC
1 ACCTAAAACAGTAAATAAAAGCATACACATAC
931204 ACCTAAAACAGTAAATAAAAGCATACACATAC
1 ACCTAAAACAGTAAATAAAAGCATACACATAC
931236 ACCTAAAACAG
1 ACCTAAAACAG
931247 ACTTTTCTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.55, C:0.21, G:0.07, T:0.17
Consensus pattern (32 bp):
ACCTAAAACAGTAAATAAAAGCATACACATAC
Found at i:934079 original size:14 final size:14
Alignment explanation
Indices: 934060--934090 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
934050 CTAAATTATT
934060 TAAATAAATTTTAA
1 TAAATAAATTTTAA
934074 TAAATAAATTTTAA
1 TAAATAAATTTTAA
934088 TAA
1 TAA
934091 TTTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAATAAATTTTAA
Found at i:934302 original size:8 final size:8
Alignment explanation
Indices: 934268--934332 Score: 53
Period size: 8 Copynumber: 8.2 Consensus size: 8
934258 TTTACATTTC
934268 AATAATAA
1 AATAATAA
*
934276 AATAA-CA
1 AATAATAA
*
934283 AATACTAA
1 AATAATAA
934291 AATAA-AA
1 AATAATAA
934298 TAATAATAA
1 -AATAATAA
*
934307 AATAATTA
1 AATAATAA
* * *
934315 ATTACTTA
1 AATAATAA
934323 AATAATAA
1 AATAATAA
934331 AA
1 AA
934333 ATTTTAATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
7 7 0.16
8 35 0.80
9 2 0.05
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (8 bp):
AATAATAA
Found at i:934307 original size:16 final size:15
Alignment explanation
Indices: 934268--934311 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
934258 TTTACATTTC
*
934268 AATAATAAAATAACA
1 AATAATAAAATAAAA
*
934283 AATACTAAAATAAAA
1 AATAATAAAATAAAA
934298 TAATAATAAAATAA
1 -AATAATAAAATAA
934312 TTAATTACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (15 bp):
AATAATAAAATAAAA
Found at i:934365 original size:12 final size:12
Alignment explanation
Indices: 934348--934372 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
934338 AATGAATAAA
934348 AAAATCAATTAT
1 AAAATCAATTAT
934360 AAAATCAATTAT
1 AAAATCAATTAT
934372 A
1 A
934373 CCTTACTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATCAATTAT
Found at i:940119 original size:21 final size:22
Alignment explanation
Indices: 940095--940135 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
940085 TCAGAATCTA
*
940095 CATAAA-AATGTTTAAAATATG
1 CATAAATAATCTTTAAAATATG
*
940116 CATAAATTATCTTTAAAATA
1 CATAAATAATCTTTAAAATA
940136 ATTATGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (22 bp):
CATAAATAATCTTTAAAATATG
Found at i:941573 original size:19 final size:18
Alignment explanation
Indices: 941549--941598 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
941539 TTTCAGAATG
941549 CAAGTTTGGTACAGGTACC
1 CAAGTTTGGTACA-GTACC
941568 CAAGTTTGGTACCAGTACC
1 CAAGTTTGGTA-CAGTACC
* *
941587 CAGGTTGGGTAC
1 CAAGTTTGGTAC
941599 CGATATCGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 1 0.04
19 25 0.89
20 2 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (18 bp):
CAAGTTTGGTACAGTACC
Found at i:948485 original size:6 final size:6
Alignment explanation
Indices: 948476--948521 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
948466 TTGACATTTT
* * *
948476 TTTCTC TTTCTC TTTCTC TTTCCC TTTCCC TTTCCC TTTCCC TTTC
1 TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC TTTC
948522 GTTTTATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (6 bp):
TTTCCC
Found at i:948957 original size:14 final size:14
Alignment explanation
Indices: 948911--948957 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
948901 GATTAAGATA
948911 ATAAATATATAATAAG
1 ATAAATA-A-AATAAG
948927 A-AAATAAAATAAG
1 ATAAATAAAATAAG
* *
948940 ATAAATAATATAAT
1 ATAAATAAAATAAG
948954 ATAA
1 ATAA
948958 TAGGAAAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 7 0.25
14 15 0.54
15 5 0.18
16 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (14 bp):
ATAAATAAAATAAG
Found at i:949404 original size:47 final size:47
Alignment explanation
Indices: 949344--949444 Score: 116
Period size: 47 Copynumber: 2.1 Consensus size: 47
949334 CTAATGCTTG
949344 AAAATAATAATAAAAATAACAATAAT-AATATTATCTTAATTCCTAAT
1 AAAATAATAATAAAAATAACAATAATAAATA-TATCTTAATTCCTAAT
* *** **
949391 AACAATAA-AATAAAGATAATTGTTTTAAATATATCTTAATTCCTAAT
1 AA-AATAATAATAAAAATAACAATAATAAATATATCTTAATTCCTAAT
949438 AAAATAA
1 AAAATAA
949445 CAAATCTAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
46 5 0.11
47 32 0.70
48 9 0.20
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (47 bp):
AAAATAATAATAAAAATAACAATAATAAATATATCTTAATTCCTAAT
Found at i:951015 original size:16 final size:16
Alignment explanation
Indices: 950994--951025 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
950984 TACAAAATCT
950994 AATAATCCATAATATA
1 AATAATCCATAATATA
*
951010 AATAATCCATTATATA
1 AATAATCCATAATATA
951026 TATATATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (16 bp):
AATAATCCATAATATA
Found at i:952729 original size:12 final size:13
Alignment explanation
Indices: 952712--952750 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
952702 TAAGCATTAA
952712 TCATGATATT-TT
1 TCATGATATTATT
952724 TCATGATATTATT
1 TCATGATATTATT
*
952737 GCTATGATATTATT
1 TC-ATGATATTATT
952751 ACATTATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 10 0.42
13 3 0.12
14 11 0.46
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.54
Consensus pattern (13 bp):
TCATGATATTATT
Found at i:953342 original size:58 final size:57
Alignment explanation
Indices: 953202--953351 Score: 144
Period size: 58 Copynumber: 2.6 Consensus size: 57
953192 CTTTGTAAGG
* ** *
953202 GAAATAAATCATTGAATTTATTTTCTTTAA-AATCATGGATGATTCTATCTTTTAAAA
1 GAAATAAATCTTTGAATTTATTTTC-TTAAGAATCATAAATGATTATATCTTTTAAAA
* ** * *
953259 GGAATTTATTTTTAAATTTATTTTTCTTAAGAAT-ATTAAATGATTATAT-TTTGTAAAA
1 GAAATAAATCTTTGAATTTA-TTTTCTTAAGAATCA-TAAATGATTATATCTTT-TAAAA
*
953317 GAAAATAAATCTTTGAATTTATTTTCCTAAGAATC
1 G-AAATAAATCTTTGAATTTATTTTCTTAAGAATC
953352 TTATACGCTT
Statistics
Matches: 72, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
57 22 0.31
58 36 0.50
59 14 0.19
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (57 bp):
GAAATAAATCTTTGAATTTATTTTCTTAAGAATCATAAATGATTATATCTTTTAAAA
Found at i:955114 original size:80 final size:80
Alignment explanation
Indices: 954981--955140 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
954971 AAAAGAGTAA
954981 GGAGTAAGAATTGAGTTTTTGACCTTGAAAAGAATTTCAATAGTTGAATGATTTAATCGAATATA
1 GGAGTAAGAATTGAGTTTTTGACCTTGAAAAGAATTTCAATAGTTGAATGATTTAATCGAATATA
955046 AACTTGAAAAACGAT
66 AACTTGAAAAACGAT
955061 GGAGTAAGAATTGAGTTTTTGACCTTGAAAAGAATTTCAATAGTTGAATGATTTAATCGAATATA
1 GGAGTAAGAATTGAGTTTTTGACCTTGAAAAGAATTTCAATAGTTGAATGATTTAATCGAATATA
955126 AACTTGAAAAACGAT
66 AACTTGAAAAACGAT
955141 TCAAAAATAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (80 bp):
GGAGTAAGAATTGAGTTTTTGACCTTGAAAAGAATTTCAATAGTTGAATGATTTAATCGAATATA
AACTTGAAAAACGAT
Found at i:970042 original size:789 final size:790
Alignment explanation
Indices: 968511--970092 Score: 2781
Period size: 789 Copynumber: 2.0 Consensus size: 790
968501 AATATCGACC
* *
968511 TAATCGTTCATCCTACTCTCGTGGTAGATCTCGTGGTAGAAGAAGAGGACGACCTCGTGTTCAGT
1 TAATCGTTCATCCTACTCTCGTGGTAGATCCCATGGTAGAAGAAGAGGACGACCTCGTGTTCAGT
* *
968576 GCCAAGTGTGTGGCAAGAATGGTCATTTGGTCAGTCAGTGCTGGAATCGGTTCGATGAGGACTTC
66 GCCAACTGTGTGGCAAGAATGGTCATTTGGTCAATCAGTGCTGGAATCGGTTCGATGAGGACTTC
* *
968641 TTTGGTATAACTCTTGATGATCATACCTCTAGCACTGAAACTTCAATAGTTTATTATGCTGCAAA
131 TCTGGTATAAATCTTGATGATCATACCTCTAGCACTGAAACTTCAATAGTTTATTATGCTGCAAA
* *
968706 TGGAACTAATGATAATGGATAAAGTTGTTTTGGTTACAATGGCAAGTACCGTGATGATAATAGGT
196 TGGAACTAATGATAATGGATAAAGTTGTTGTGGTTACAATGGCAAGTACCGTGATGATAATAGGA
** *
968771 CTGTTGGCCAAACTCAGGCTCATGTTGTTACTTCTGGCCAATATCAATGGGTGGTTGACTCTGGT
261 CTACTGGCAAAACTCAGGCTCATGTTGTTACTTCTGGCCAATATCAATGGGTGGTTGACTCTGGT
*
968836 GAAACTCACCATGTTACTTCCAATGCTGCTTCTATCACTCATCACACTAGTTGCAGTAATCCTGA
326 GAAACTCACCATGTTACTTCCAATGCTGCTTCGATCACTCATCACACTAGTTGCAGTAATCCTGA
968901 TAAGTTAATGGTAGGGAATGATGATTTTTGCCTGTTAATATGATTGGTCAGACTGAGTTACTTGC
391 TAAGTTAATGGTAGGGAATGATGATTTTTGCCTGTTAATATGATTGGTCAGACTGAGTTACTTGC
*
968966 TTCATCACGCACTTTGTCTTTTAATGAAATTCTACATGTTCATTCTATAACTAAGAATATACTTT
456 TTCATCAAGCACTTTGTCTTTTAATGAAATTCTACATGTTCATTCTATAACTAAGAATATACTTT
* *
969031 CTGTATCTAAGCTTGCTAGGGATAACCATGTGTTTCTTGAGTTTCATGCAAAAACTTGCTATGTT
521 CTGTATCTAAGCTTGCTAGGGATAACCATGTGTTTCTTCAATTTCATGCAAAAACTTGCTATGTT
* * *
969096 CGAGATGAAGTCACTAAGGTTGTTTTGCTGCGATGAAAAGAATGTGATGGTTTATATGTTTTCAA
586 CGAGATGAAGTCACTAAGGTTGTTTTGATGCGAGGAAAAGAATGTGATGGTTTATATATTTTCAA
969161 GTCTAGCAGTTCTCAAGGTGTAGCTGGCATGACTGAAGTGCATTATGCCATGACATCCTCTAAGG
651 GTCTAGCAGTTCTCAAGGTGTAGCTGGCATGACTGAAGTGCATTATGCCATGACATCCTCTAAGG
* ** *
969226 CTTCTGAAATATGGCATAGGTGACTTGGTCATCCTGTCTATGATACTCTTATGAAAGTTTGTAAA
716 CTTATGAAATATGGCATAGACGACTTGGTCATCCTGCCTATGATACTCTTATGAAAGTTTGTAAA
969291 CAAATTAATG
781 CAAATTAATG
* *
969301 TAATTGTTCATCCTACTCTCGTGGTAGATCCCATGGTAGAGGAAGAGGACGACCTCGTGTTCAGT
1 TAATCGTTCATCCTACTCTCGTGGTAGATCCCATGGTAGAAGAAGAGGACGACCTCGTGTTCAGT
* * *
969366 GCTAACTGTTTGGCAAGAAT-GTCCTTTGGTCAATCAGTGCTGGAATCGGTTCGATGAGGACTTC
66 GCCAACTGTGTGGCAAGAATGGTCATTTGGTCAATCAGTGCTGGAATCGGTTCGATGAGGACTTC
*
969430 TCTGGTATAAATCTTGATGATCATACCTCTAGCACTGAAACTTCAATAGTTTATTATGTTGCAAA
131 TCTGGTATAAATCTTGATGATCATACCTCTAGCACTGAAACTTCAATAGTTTATTATGCTGCAAA
* **
969495 TGGAACTAGTGATAATGGATGTAGTTGTTGTGGTTACAATGGCAAGTACCGTGATGATAATAGGA
196 TGGAACTAATGATAATGGATAAAGTTGTTGTGGTTACAATGGCAAGTACCGTGATGATAATAGGA
*
969560 CTACTGGGAAAACTCAGGCTCATGTTGTTACTTCTGGCCAATATCAATGGGTGGTTGACTCTGGT
261 CTACTGGCAAAACTCAGGCTCATGTTGTTACTTCTGGCCAATATCAATGGGTGGTTGACTCTGGT
* * *
969625 GCAACTCACCATGTTACTTCTAATGCTGCTTCGATCACTCATGACACTAGTTGCAGTAATCCTGA
326 GAAACTCACCATGTTACTTCCAATGCTGCTTCGATCACTCATCACACTAGTTGCAGTAATCCTGA
* *
969690 TAAGTTAATGGTAGGGAATGGTGATTTTTTGCCTGTTACTATGATTGGTCAGACTGAGTTACTTG
391 TAAGTTAATGGTAGGGAATGATGA-TTTTTGCCTGTTAATATGATTGGTCAGACTGAGTTACTTG
*
969755 CTTCATCAAGCACTTTGTCTTTTAATGAAATTCTACATGTTCCTTCTATAACTAAGAATATACTT
455 CTTCATCAAGCACTTTGTCTTTTAATGAAATTCTACATGTTCATTCTATAACTAAGAATATACTT
969820 TCTGTATCTAAGCTTGCTAGGGATAACCATGTGTTTCTTCAATTTCATGCAAAAACTTGCTATGT
520 TCTGTATCTAAGCTTGCTAGGGATAACCATGTGTTTCTTCAATTTCATGCAAAAACTTGCTATGT
*
969885 TCGAGATGAAGTCACTAAGGTTGTTTTGATGCGAGGAGAAGAATGTGATGGTTTATATATTTTCA
585 TCGAGATGAAGTCACTAAGGTTGTTTTGATGCGAGGAAAAGAATGTGATGGTTTATATATTTTCA
969950 AGTCTA-CAGTTCTCAAGGTGTAGCTGGCATGACTGAAGTGCATTATGCCATGACATCCTCTAAG
650 AGTCTAGCAGTTCTCAAGGTGTAGCTGGCATGACTGAAGTGCATTATGCCATGACATCCTCTAAG
*
970014 GCTTATGAAATCTGGCATAGACGACTTGGTCATCCTGCCTATGATACTCTTATGAAAGTTTGTAA
715 GCTTATGAAATATGGCATAGACGACTTGGTCATCCTGCCTATGATACTCTTATGAAAGTTTGTAA
970079 ACAAATTAATG
780 ACAAATTAATG
970090 TAA
1 TAA
970093 AACCCTTTCA
Statistics
Matches: 751, Mismatches: 40, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
789 441 0.59
790 310 0.41
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (790 bp):
TAATCGTTCATCCTACTCTCGTGGTAGATCCCATGGTAGAAGAAGAGGACGACCTCGTGTTCAGT
GCCAACTGTGTGGCAAGAATGGTCATTTGGTCAATCAGTGCTGGAATCGGTTCGATGAGGACTTC
TCTGGTATAAATCTTGATGATCATACCTCTAGCACTGAAACTTCAATAGTTTATTATGCTGCAAA
TGGAACTAATGATAATGGATAAAGTTGTTGTGGTTACAATGGCAAGTACCGTGATGATAATAGGA
CTACTGGCAAAACTCAGGCTCATGTTGTTACTTCTGGCCAATATCAATGGGTGGTTGACTCTGGT
GAAACTCACCATGTTACTTCCAATGCTGCTTCGATCACTCATCACACTAGTTGCAGTAATCCTGA
TAAGTTAATGGTAGGGAATGATGATTTTTGCCTGTTAATATGATTGGTCAGACTGAGTTACTTGC
TTCATCAAGCACTTTGTCTTTTAATGAAATTCTACATGTTCATTCTATAACTAAGAATATACTTT
CTGTATCTAAGCTTGCTAGGGATAACCATGTGTTTCTTCAATTTCATGCAAAAACTTGCTATGTT
CGAGATGAAGTCACTAAGGTTGTTTTGATGCGAGGAAAAGAATGTGATGGTTTATATATTTTCAA
GTCTAGCAGTTCTCAAGGTGTAGCTGGCATGACTGAAGTGCATTATGCCATGACATCCTCTAAGG
CTTATGAAATATGGCATAGACGACTTGGTCATCCTGCCTATGATACTCTTATGAAAGTTTGTAAA
CAAATTAATG
Found at i:971900 original size:62 final size:63
Alignment explanation
Indices: 971803--971928 Score: 236
Period size: 62 Copynumber: 2.0 Consensus size: 63
971793 TTTTAAAGAA
971803 TCACGAGCTGATGTGTCTTTGGTTATCAAGAAAATGGGTGTTCACTACACGTAT-TACTTGTG
1 TCACGAGCTGATGTGTCTTTGGTTATCAAGAAAATGGGTGTTCACTACACGTATCTACTTGTG
*
971865 TCACGAGCTGATGTGTCTTTGTTTATCAAGAAAATGGGTGTTCACTACACGTATCTACTTGTG
1 TCACGAGCTGATGTGTCTTTGGTTATCAAGAAAATGGGTGTTCACTACACGTATCTACTTGTG
971928 T
1 T
971929 ATGTTGATGA
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
62 53 0.85
63 9 0.15
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.37
Consensus pattern (63 bp):
TCACGAGCTGATGTGTCTTTGGTTATCAAGAAAATGGGTGTTCACTACACGTATCTACTTGTG
Found at i:975597 original size:15 final size:15
Alignment explanation
Indices: 975573--975635 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
975563 TATATTTAAT
975573 ATTTTATTTTTGATG
1 ATTTTATTTTTGATG
975588 ATTTT-TTTTTG-TG
1 ATTTTATTTTTGATG
*
975601 AACTTTT-TTTTTGGTG
1 -A-TTTTATTTTTGATG
**
975617 AACTTATTTTTGATG
1 ATTTTATTTTTGATG
975632 ATTT
1 ATTT
975636 GATATGGTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
13 2 0.05
14 9 0.23
15 26 0.67
16 2 0.05
ACGTcount: A:0.17, C:0.03, G:0.14, T:0.65
Consensus pattern (15 bp):
ATTTTATTTTTGATG
Found at i:975608 original size:16 final size:16
Alignment explanation
Indices: 975589--975627 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 16
975579 TTTTTGATGA
975589 TTTTTTTTT-GTGAAC
1 TTTTTTTTTGGTGAAC
975604 TTTTTTTTTGGTGAAC
1 TTTTTTTTTGGTGAAC
975620 TTATTTTT
1 TT-TTTTT
975628 GATGATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 9 0.41
16 8 0.36
17 5 0.23
ACGTcount: A:0.13, C:0.05, G:0.13, T:0.69
Consensus pattern (16 bp):
TTTTTTTTTGGTGAAC
Found at i:976562 original size:31 final size:31
Alignment explanation
Indices: 976524--976582 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
976514 ACTACATTTT
976524 AATTAAATAAAAACAAAAGAGACCAAATCTA
1 AATTAAATAAAAACAAAAGAGACCAAATCTA
* * *
976555 AATTAAATAAAAACTAAAGCGATCAAAT
1 AATTAAATAAAAACAAAAGAGACCAAAT
976583 ATTATGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.63, C:0.12, G:0.07, T:0.19
Consensus pattern (31 bp):
AATTAAATAAAAACAAAAGAGACCAAATCTA
Found at i:979964 original size:201 final size:197
Alignment explanation
Indices: 979568--979966 Score: 737
Period size: 201 Copynumber: 2.0 Consensus size: 197
979558 AGAATTTGTG
979568 ATATTTTTCAGTGAAACACACACTGAATTTGCGTTGAAGAGGTCAATATGATGAACTAGAAATTT
1 ATATTTTTCAGTGAAACACACACTGAATTTGCGTTGAAGAGGTCAATATGATGAACTAGAAATTT
979633 TGAGTCCAACGGTTATGATTACGACGTTCAACAATAACCAGTGATGAAATTGATGATGGTAGTGA
66 TGAGTCCAACGGTTATGATTACGACGTTCAACAATAACCAGTGATGAAATTGATGATGGTAGTGA
*
979698 TGATAATGAGCGACGGCCATTAATAGGGAGTTTAACTGAATTTAAGGTCAAATTTATATTTATCT
131 CGATAATGAGCGACGGCCATTAATAGGGAGTTTAACTGAATTTAAGGTCAAATTTATATTTATCT
979763 AA
196 AA
979765 ATATTTTTCAGTGAAACACACACTGAATTTGCGTTGAAGAGGTCAATATGAGTGAACTAGAAATT
1 ATATTTTTCAGTGAAACACACACTGAATTTGCGTTGAAGAGGTCAATATGA-TGAACTAGAAA-T
979830 TTTGAGTCCAACGGTTAATGATTACGACGTTCAACAATAACCAGTGATGAAATTGATGATGGCTA
64 TTTGAGTCCAACGGTT-ATGATTACGACGTTCAACAATAACCAGTGATGAAATTGATGATGG-TA
979895 GTGACGATAATGAGCGACGGCCATTAATAGGGAGTTTAACTGAATTTAAAGGTCAAATTTATA-T
127 GTGACGATAATGAGCGACGGCCATTAATAGGGAGTTTAACTGAATTT-AAGGTCAAATTTATATT
979959 TATCTAA
191 TATCTAA
979966 A
1 A
979967 GTTTAAGGGT
Statistics
Matches: 196, Mismatches: 1, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
197 51 0.26
198 11 0.06
199 17 0.09
200 45 0.23
201 57 0.29
202 15 0.08
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (197 bp):
ATATTTTTCAGTGAAACACACACTGAATTTGCGTTGAAGAGGTCAATATGATGAACTAGAAATTT
TGAGTCCAACGGTTATGATTACGACGTTCAACAATAACCAGTGATGAAATTGATGATGGTAGTGA
CGATAATGAGCGACGGCCATTAATAGGGAGTTTAACTGAATTTAAGGTCAAATTTATATTTATCT
AA
Found at i:980491 original size:2 final size:2
Alignment explanation
Indices: 980484--980512 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
980474 TAAAATAATC
980484 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
980513 TTAAAATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:981733 original size:30 final size:29
Alignment explanation
Indices: 981687--981745 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
981677 ACTAAATAAT
* *
981687 TTGTTACAATTTTTTATTATGAAGAATATTA
1 TTGTCACAATTTTTTATAATG-AGAA-ATTA
981718 TTGTCACAA-TTTTTATAATGAGAAATTA
1 TTGTCACAATTTTTTATAATGAGAAATTA
981746 ATATTTGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 4 0.15
29 4 0.15
30 10 0.38
31 8 0.31
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.47
Consensus pattern (29 bp):
TTGTCACAATTTTTTATAATGAGAAATTA
Found at i:982922 original size:23 final size:23
Alignment explanation
Indices: 982894--982940 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
982884 CAGTAAAAAA
982894 AATAATAGTAGAAAATAAGAGAT
1 AATAATAGTAGAAAATAAGAGAT
*
982917 AATAATAGTATAAAATAAGAGAT
1 AATAATAGTAGAAAATAAGAGAT
982940 A
1 A
982941 GGAAAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (23 bp):
AATAATAGTAGAAAATAAGAGAT
Found at i:983468 original size:15 final size:15
Alignment explanation
Indices: 983450--983481 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
983440 ATACTAATAG
*
983450 TGACAAAATTAATTT
1 TGACAAAATTAAATT
983465 TGACAAAATTAAATT
1 TGACAAAATTAAATT
983480 TG
1 TG
983482 TCATAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (15 bp):
TGACAAAATTAAATT
Found at i:986901 original size:21 final size:20
Alignment explanation
Indices: 986877--986976 Score: 72
Period size: 18 Copynumber: 5.2 Consensus size: 20
986867 GAGTACAAGT
986877 AGAAATTCTAAAAGAACAATA
1 AGAAA-TCTAAAAGAACAATA
*
986898 AGAAA-C-AAAA-TACAAT-
1 AGAAATCTAAAAGAACAATA
*
986914 -CAAATCTAAAAGAACAATA
1 AGAAATCTAAAAGAACAATA
* *
986933 AGAAA-C-AAATACATCAA-A
1 AGAAATCTAAA-AGAACAATA
986951 TAGCAAATCTAAAAGAACAATA
1 -AG-AAATCTAAAAGAACAATA
986973 AGAA
1 AGAA
986977 CAAAATCAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 23
0.66 0.09 0.25
Matches are distributed among these distances:
15 3 0.05
16 1 0.02
17 9 0.15
18 13 0.22
19 9 0.15
20 8 0.13
21 13 0.22
22 4 0.07
ACGTcount: A:0.64, C:0.13, G:0.08, T:0.15
Consensus pattern (20 bp):
AGAAATCTAAAAGAACAATA
Found at i:986958 original size:40 final size:38
Alignment explanation
Indices: 986883--986993 Score: 153
Period size: 35 Copynumber: 3.0 Consensus size: 38
986873 AAGTAGAAAT
986883 TCTAAAAGAACAATAAGAAAC-AAAAT-ACAAT--CAAA
1 TCTAAAAGAACAATAAGAAACAAAAATCA-AATAGCAAA
986918 TCTAAAAGAACAATAAGAAACAAATACATCAAATAGCAAA
1 TCTAAAAGAACAATAAGAAACAAA-A-ATCAAATAGCAAA
986958 TCTAAAAGAACAATAAG-AAC-AAAATCAAATAGCAAA
1 TCTAAAAGAACAATAAGAAACAAAAATCAAATAGCAAA
986994 GCCTGGCTAG
Statistics
Matches: 70, Mismatches: 0, Indels: 11
0.86 0.00 0.14
Matches are distributed among these distances:
35 21 0.30
36 15 0.21
37 2 0.03
38 7 0.10
39 4 0.06
40 21 0.30
ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14
Consensus pattern (38 bp):
TCTAAAAGAACAATAAGAAACAAAAATCAAATAGCAAA
Found at i:988593 original size:22 final size:23
Alignment explanation
Indices: 988545--988598 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
988535 AATTATCTTT
988545 AATTTTT-GGATTTAATTCAAAC
1 AATTTTTAGGATTTAATTCAAAC
*
988567 AATTTTTAGGATTTATCTTC-AAC
1 AATTTTTAGGATTTA-ATTCAAAC
988590 -ATTTTTAGG
1 AATTTTTAGG
988599 GCTTGTAGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 16 0.55
23 10 0.34
24 3 0.10
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.48
Consensus pattern (23 bp):
AATTTTTAGGATTTAATTCAAAC
Found at i:995165 original size:27 final size:26
Alignment explanation
Indices: 995110--995168 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
995100 AAAGAGGAGA
* * *
995110 AAAGAGAATTAAAATCATGCGCAAGG
1 AAAGAGAATTAAAATCAAGAGCAAAG
995136 AAAGAGAATTAGAAATCAAGAG-AGAAG
1 AAAGAGAATTA-AAATCAAGAGCA-AAG
995163 AAAGAG
1 AAAGAG
995169 GAAGAAAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 12 0.43
27 16 0.57
ACGTcount: A:0.56, C:0.07, G:0.25, T:0.12
Consensus pattern (26 bp):
AAAGAGAATTAAAATCAAGAGCAAAG
Found at i:998707 original size:22 final size:22
Alignment explanation
Indices: 998682--998723 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
998672 ATTCTATATT
998682 CTTCCACTACCTTAGCTATCTA
1 CTTCCACTACCTTAGCTATCTA
998704 CTTCCACTACCTTAGCTATC
1 CTTCCACTACCTTAGCTATC
998724 CACACTAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.38, G:0.05, T:0.36
Consensus pattern (22 bp):
CTTCCACTACCTTAGCTATCTA
Found at i:1001987 original size:22 final size:21
Alignment explanation
Indices: 1001917--1001997 Score: 67
Period size: 22 Copynumber: 3.8 Consensus size: 21
1001907 CAGAACCCCA
*
1001917 GGGGGTATCGATTCCCCTATGG
1 GGGGGAATCGATTCCCCTAT-G
* **
1001939 GGGGGAATCGGTTCCCCTTTAAA
1 GGGGGAATCGATTCCCC--TATG
*
1001962 GGGGGAATCGGTT-CCCTCATG
1 GGGGGAATCGATTCCCCT-ATG
1001983 GGGGG-ATCGATTCCC
1 GGGGGAATCGATTCCC
1001998 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 7 0.15
21 8 0.17
22 18 0.38
23 13 0.27
24 2 0.04
ACGTcount: A:0.16, C:0.23, G:0.36, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGATTCCCCTATG
Found at i:1001991 original size:20 final size:20
Alignment explanation
Indices: 1001962--1001999 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1001952 CCCCTTTAAA
*
1001962 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
1001982 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
1002000 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:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:1011395 original size:30 final size:30
Alignment explanation
Indices: 1011359--1011420 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1011349 CTTCAACTTG
*
1011359 TTTTTATATGTTGGA-ATGAGTTTGTAGCCA
1 TTTTTATATGTTGGAGATG-GTTTGAAGCCA
* *
1011389 TTTTTATCTGTTGGAGATGTTTTGAAGCCA
1 TTTTTATATGTTGGAGATGGTTTGAAGCCA
1011419 TT
1 TT
1011421 GGGGATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 25 0.89
31 3 0.11
ACGTcount: A:0.21, C:0.08, G:0.23, T:0.48
Consensus pattern (30 bp):
TTTTTATATGTTGGAGATGGTTTGAAGCCA
Found at i:1018638 original size:2 final size:2
Alignment explanation
Indices: 1018631--1018705 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
1018621 AAAACATGCA
1018631 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1018673 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1018706 ATGATATACT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1019232 original size:21 final size:19
Alignment explanation
Indices: 1019199--1019244 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
1019189 CTATGGGTAC
1019199 CGATACTGACCCTTTAGTAT
1 CGATACTGACCC-TTAGTAT
* *
1019219 CGATATTGAACCCTTGGTAT
1 CGATACTG-ACCCTTAGTAT
1019239 CGATAC
1 CGATAC
1019245 CCACCCTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (19 bp):
CGATACTGACCCTTAGTAT
Found at i:1021969 original size:127 final size:127
Alignment explanation
Indices: 1021743--1022001 Score: 518
Period size: 127 Copynumber: 2.0 Consensus size: 127
1021733 CCAGATTCGA
1021743 GCAGTGATGTCTGCAAGGTGTTTGTACACTCATTATCAACGAAAATACAAAGAAAATACTTAAAT
1 GCAGTGATGTCTGCAAGGTGTTTGTACACTCATTATCAACGAAAATACAAAGAAAATACTTAAAT
1021808 TAAATGACAGCTACAACAGAAGTTACTAACATGTTCACCAACAATCATTTTATCCATTCCTT
66 TAAATGACAGCTACAACAGAAGTTACTAACATGTTCACCAACAATCATTTTATCCATTCCTT
1021870 GCAGTGATGTCTGCAAGGTGTTTGTACACTCATTATCAACGAAAATACAAAGAAAATACTTAAAT
1 GCAGTGATGTCTGCAAGGTGTTTGTACACTCATTATCAACGAAAATACAAAGAAAATACTTAAAT
1021935 TAAATGACAGCTACAACAGAAGTTACTAACATGTTCACCAACAATCATTTTATCCATTCCTT
66 TAAATGACAGCTACAACAGAAGTTACTAACATGTTCACCAACAATCATTTTATCCATTCCTT
1021997 GCAGT
1 GCAGT
1022002 TGCTTTTCGC
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 132 1.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (127 bp):
GCAGTGATGTCTGCAAGGTGTTTGTACACTCATTATCAACGAAAATACAAAGAAAATACTTAAAT
TAAATGACAGCTACAACAGAAGTTACTAACATGTTCACCAACAATCATTTTATCCATTCCTT
Found at i:1026886 original size:4 final size:4
Alignment explanation
Indices: 1026877--1026930 Score: 83
Period size: 4 Copynumber: 13.5 Consensus size: 4
1026867 TCATTCTAAA
*
1026877 ATTT ATTT ATTTT ATTT ATTT ATTT ATTT ATTT ATTT A-TT ATTT AATT
1 ATTT ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1026925 ATTT AT
1 ATTT AT
1026931 ATTTGTTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 3 0.07
4 39 0.85
5 4 0.09
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:1026940 original size:19 final size:19
Alignment explanation
Indices: 1026878--1026971 Score: 61
Period size: 17 Copynumber: 4.8 Consensus size: 19
1026868 CATTCTAAAA
*
1026878 TTTATTTATTT-TATTTA-
1 TTTAATTATTTATATTTAT
*
1026895 TTTATTTATTTATTTATTTATT
1 TTTAATTATTTA--TATTTA-T
*
1026917 ATTTAATTATTTATATTTGT
1 -TTTAATTATTTATATTTAT
*
1026937 TTTAA-AATTT-TATTTAT
1 TTTAATTATTTATATTTAT
*
1026954 GTTAATCTATTTTATATT
1 TTTAAT-TA-TTTATATT
1026972 ATTAATATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
17 21 0.34
18 4 0.07
19 6 0.10
20 10 0.16
21 9 0.15
23 11 0.18
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTAATTATTTATATTTAT
Found at i:1028918 original size:30 final size:30
Alignment explanation
Indices: 1028884--1028946 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
1028874 TTTAAAAGAT
1028884 TAATTTTTTCCGAATAATTTAGAACACTTA
1 TAATTTTTTCCGAATAATTTAGAACACTTA
1028914 TAATTTTTTCCGAATAATTTAGAACACTTA
1 TAATTTTTTCCGAATAATTTAGAACACTTA
1028944 TAA
1 TAA
1028947 AGTAATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (30 bp):
TAATTTTTTCCGAATAATTTAGAACACTTA
Found at i:1031499 original size:37 final size:37
Alignment explanation
Indices: 1031457--1031558 Score: 161
Period size: 37 Copynumber: 2.8 Consensus size: 37
1031447 TAGGTAATCA
*
1031457 GTCCATATGTCCCGAAGAACATAGGTAATCTATACCT
1 GTCCATATGTCCCGAAGAACATAGGTAATCTATAACT
*
1031494 GTCCATATGTCCCGAAGAACATAGGTAATCTGTAACT
1 GTCCATATGTCCCGAAGAACATAGGTAATCTATAACT
*
1031531 GTCCATATGTTCC-ACAGAACATAGGTAA
1 GTCCATATGTCCCGA-AGAACATAGGTAA
1031559 CCCTCGACTC
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 1 0.02
37 60 0.98
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (37 bp):
GTCCATATGTCCCGAAGAACATAGGTAATCTATAACT
Found at i:1031950 original size:2 final size:2
Alignment explanation
Indices: 1031943--1031977 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1031933 CTTATGTCAT
1031943 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
1031978 CTCTATGTTC
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:1035001 original size:23 final size:24
Alignment explanation
Indices: 1034953--1035013 Score: 88
Period size: 23 Copynumber: 2.6 Consensus size: 24
1034943 GTGTATATTT
*
1034953 AACTATTTTCAATCCTCTTTAAAA
1 AACTATTTTCAATCCTCATTAAAA
*
1034977 AACTATTTTCAGTCCT-ATTAAAA
1 AACTATTTTCAATCCTCATTAAAA
*
1035000 AATTATTTTCAATC
1 AACTATTTTCAATC
1035014 ATCAAATTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
23 18 0.55
24 15 0.45
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.43
Consensus pattern (24 bp):
AACTATTTTCAATCCTCATTAAAA
Found at i:1036370 original size:18 final size:18
Alignment explanation
Indices: 1036347--1036385 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1036337 ACCGGTCACA
1036347 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1036365 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1036383 ACC
1 ACC
1036386 GTTGACCCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.51, G:0.21, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1037737 original size:18 final size:18
Alignment explanation
Indices: 1037711--1037746 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1037701 TCGAAAGGAC
*
1037711 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1037729 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1037747 CGGATGGAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1038980 original size:24 final size:24
Alignment explanation
Indices: 1038874--1038980 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
1038864 ATATTTTATC
*
1038874 TGATTTCTGATTTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTT
** * * *
1038898 TGACATCTGATCTGAAATCTGTTC
1 TGATTTCTGATCTGAATTATGTTT
* * * * * *
1038922 TGATTCCTAACCTGGATTCTGTTA
1 TGATTTCTGATCTGAATTATGTTT
*
1038946 TGATATCTGATCTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTT
*
1038970 TGATTTTTGAT
1 TGATTTCTGAT
1038981 ATCTCCGTTT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTATGTTT
Found at i:1039146 original size:2 final size:2
Alignment explanation
Indices: 1039139--1039164 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1039129 ACGGATGGGG
1039139 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
1039165 GTTTTAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1041136 original size:18 final size:18
Alignment explanation
Indices: 1041113--1041151 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1041103 ACCGGTCACA
1041113 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1041131 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1041149 ACC
1 ACC
1041152 GTTGACCCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.51, G:0.21, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1042504 original size:18 final size:18
Alignment explanation
Indices: 1042478--1042513 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1042468 TCGAAAGGAC
*
1042478 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1042496 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1042514 CGGATGGAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1043745 original size:24 final size:24
Alignment explanation
Indices: 1043639--1043745 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
1043629 ATATTTTATC
*
1043639 TGATTTCTGATTTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTT
** * * *
1043663 TGACATCTGATCTGAAATCTGTTC
1 TGATTTCTGATCTGAATTATGTTT
* * * * * *
1043687 TGATTCCTAACCTGGATTCTGTTA
1 TGATTTCTGATCTGAATTATGTTT
*
1043711 TGATATCTGATCTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTT
*
1043735 TGATTTTTGAT
1 TGATTTCTGAT
1043746 ATCTCCGTTT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTATGTTT
Found at i:1043913 original size:2 final size:2
Alignment explanation
Indices: 1043906--1043932 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1043896 CGGATGGGGG
1043906 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 T
1043933 GTTTTAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1047913 original size:16 final size:16
Alignment explanation
Indices: 1047892--1047925 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1047882 TATCGTCGAC
1047892 CAAATTTTACTATGCA
1 CAAATTTTACTATGCA
*
1047908 CAAATTTTACTATTCA
1 CAAATTTTACTATGCA
1047924 CA
1 CA
1047926 TAAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (16 bp):
CAAATTTTACTATGCA
Found at i:1055763 original size:2 final size:2
Alignment explanation
Indices: 1055758--1055782 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1055748 TAATTTAAAC
1055758 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 T
1055783 TACCGGATCG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1056203 original size:2 final size:2
Alignment explanation
Indices: 1056196--1056221 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1056186 GATAATGTAA
1056196 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
1056222 GCAGATCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1064409 original size:21 final size:21
Alignment explanation
Indices: 1064371--1064410 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1064361 TCTAAAGCGA
*
1064371 TTGTTCATCATCTTTTTCAGT
1 TTGTTCATCATCTCTTTCAGT
* *
1064392 TTGTTTATCTTCTCTTTCA
1 TTGTTCATCATCTCTTTCA
1064411 CGTCTATAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.12, C:0.20, G:0.07, T:0.60
Consensus pattern (21 bp):
TTGTTCATCATCTCTTTCAGT
Found at i:1065626 original size:19 final size:19
Alignment explanation
Indices: 1065602--1065638 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1065592 TATTGGAATA
*
1065602 TGCATTCTAGAATATGCAG
1 TGCATTCTAGAACATGCAG
1065621 TGCATTCTAGAACATGCA
1 TGCATTCTAGAACATGCA
1065639 CTGCTAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (19 bp):
TGCATTCTAGAACATGCAG
Found at i:1065912 original size:31 final size:31
Alignment explanation
Indices: 1065851--1065912 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
1065841 TGGTATCAAA
****
1065851 GATTAATATTGGAATTAATATTGGGTAAAAT
1 GATTAATATTGGAATTAATAAAAAGTAAAAT
1065882 GATTAATATTGGAATTAATTAAAAAG-AAAAT
1 GATTAATATTGGAATTAA-TAAAAAGTAAAAT
1065913 AGTGGGTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.35
Consensus pattern (31 bp):
GATTAATATTGGAATTAATAAAAAGTAAAAT
Found at i:1067792 original size:2 final size:2
Alignment explanation
Indices: 1067785--1067829 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1067775 AAAAGAAATA
1067785 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1067827 AT A
1 AT A
1067830 GAGTAGTATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1068962 original size:35 final size:36
Alignment explanation
Indices: 1068874--1068971 Score: 108
Period size: 35 Copynumber: 2.6 Consensus size: 36
1068864 AAAATTAAAA
*
1068874 TTTAAAATTATATACTATATATATGTTTTAAAAAAATATT
1 TTTAAAATTATATA--ATATATA--TTTTAAAAAAATAGT
* * *
1068914 TTTAAAATCATATAATATATATTTTCAAATAAT-GT
1 TTTAAAATTATATAATATATATTTTAAAAAAATAGT
*
1068949 TTTAAAATTATATATTATATATT
1 TTTAAAATTATATAATATATATT
1068972 ATTATATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
35 22 0.42
36 10 0.19
38 7 0.13
40 13 0.25
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (36 bp):
TTTAAAATTATATAATATATATTTTAAAAAAATAGT
Found at i:1069008 original size:87 final size:85
Alignment explanation
Indices: 1068889--1069054 Score: 235
Period size: 87 Copynumber: 1.9 Consensus size: 85
1068879 AATTATATAC
* * *
1068889 TATATATATGTTTTAAAAAAATATTTTTAAAATCATATAATATATATTTTCAAATAATGTTTT-A
1 TATATATATCTTTTAAAAAAATATTTTCAAAATCATATAATATATAGTTTCAAA-AATGTTTTAA
*
1068953 AAATTATATATTATATATTAT
65 AAACTATATATTATATATTAT
* * *
1068974 TATATATATACTTTCTAAAAAAATGTTTTCAAAATCATATACTATATAGTTTCCAAAATGTTTTA
1 TATATATAT-CTTT-TAAAAAAATATTTTCAAAATCATATAATATATAGTTTCAAAAATGTTTTA
1069039 AAAACTATATATTATA
64 AAAACTATATATTATA
1069055 AATATTTTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
85 9 0.13
86 11 0.15
87 51 0.72
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (85 bp):
TATATATATCTTTTAAAAAAATATTTTCAAAATCATATAATATATAGTTTCAAAAATGTTTTAAA
AACTATATATTATATATTAT
Found at i:1069032 original size:35 final size:36
Alignment explanation
Indices: 1068993--1069140 Score: 99
Period size: 35 Copynumber: 4.1 Consensus size: 36
1068983 ACTTTCTAAA
*
1068993 AAAATGTTTTCAAAA-TCATATACTAT-ATAGTTTCC
1 AAAATGTTTTAAAAACT-ATATACTATAATAGTTTCC
* * *
1069028 AAAATGTTTTAAAAACTATATATTATAAATATTTTTC
1 AAAATGTTTTAAAAACTATATACTAT-AATAGTTTCC
** * *
1069065 AAAATGTTTTTTTAAATTATATATTATATATA-TTT-C
1 AAAATG-TTTTAAAAACTATATACTATA-ATAGTTTCC
* ** * *
1069101 AAAATATTTTTTAAACTATATAATAT-ATATGTTTTC
1 AAAATGTTTTAAAAACTATATACTATAATA-GTTTCC
1069137 AAAA
1 AAAA
1069141 ACTATATATA
Statistics
Matches: 95, Mismatches: 10, Indels: 15
0.79 0.08 0.12
Matches are distributed among these distances:
33 3 0.03
35 43 0.45
36 12 0.13
37 17 0.18
38 20 0.21
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (36 bp):
AAAATGTTTTAAAAACTATATACTATAATAGTTTCC
Found at i:1069101 original size:36 final size:35
Alignment explanation
Indices: 1069016--1069140 Score: 133
Period size: 35 Copynumber: 3.4 Consensus size: 35
1069006 AATCATATAC
**
1069016 TATATAGTTTCCAAAATGTTTTAAAAACTATATATTA
1 TATATA-TTT-CAAAATGTTTTTTAAACTATATATTA
* *
1069053 TAAATATTTTTCAAAATGTTTTTTTAAATTATATATTA
1 T--ATATATTTCAAAATG-TTTTTTAAACTATATATTA
* *
1069091 TATATATTTCAAAATATTTTTTAAACTATATAATA
1 TATATATTTCAAAATGTTTTTTAAACTATATATTA
*
1069126 TATATGTTTTCAAAA
1 TATAT-ATTTCAAAA
1069141 ACTATATATA
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
35 22 0.29
36 21 0.28
37 8 0.11
38 20 0.27
39 4 0.05
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (35 bp):
TATATATTTCAAAATGTTTTTTAAACTATATATTA
Found at i:1069135 original size:23 final size:23
Alignment explanation
Indices: 1069104--1069153 Score: 57
Period size: 26 Copynumber: 2.1 Consensus size: 23
1069094 ATATTTCAAA
*
1069104 ATAT-TTTTTAAACTATATAATAT
1 ATATGTTTTAAAACTATAT-ATAT
1069127 ATATGTTTTCAAAAACTATATATAT
1 ATATGTTTT--AAAACTATATATAT
1069152 AT
1 AT
1069154 TTCCAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 4 0.17
24 4 0.17
25 6 0.26
26 9 0.39
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATGTTTTAAAACTATATATAT
Found at i:1070374 original size:9 final size:8
Alignment explanation
Indices: 1070347--1070407 Score: 52
Period size: 9 Copynumber: 7.1 Consensus size: 8
1070337 TTTCTAAAAG
*
1070347 AAATAACA
1 AAATAATA
1070355 AAATAATA
1 AAATAATA
1070363 AAATATATA
1 AAATA-ATA
*
1070372 AAA-ATTA
1 AAATAATA
1070379 GGAAATAATA
1 --AAATAATA
1070389 ATAATAATA
1 A-AATAATA
1070398 ATAATAATA
1 A-AATAATA
1070407 A
1 A
1070408 TAATTTGTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
7 2 0.04
8 14 0.31
9 26 0.58
10 3 0.07
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (8 bp):
AAATAATA
Found at i:1070390 original size:3 final size:3
Alignment explanation
Indices: 1070382--1070411 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1070372 AAAATTAGGA
1070382 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1070412 TTGTATTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1071902 original size:84 final size:84
Alignment explanation
Indices: 1071784--1072316 Score: 687
Period size: 84 Copynumber: 6.4 Consensus size: 84
1071774 TCCTGTTAGT
* * * * ** *
1071784 AGATAGCTCTTCTCGCCTTGAGCTATGCTTCAAATAATGCACCTTTGAGTTGAGTGTAATCGAAC
1 AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* *
1071849 TCGAATGTCTTTTATTGGC
66 TCGAAGGTCTTTTGTTGGC
* * * * *
1071868 AGATAACCCTTCTAGCCTTGAGCTAAGCTACAAATGATGTGCCTTTGAGCTGAATGTAATCGAAC
1 AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* *
1071933 TCGAAGG---TTTGCTGAC
66 TCGAAGGTCTTTTGTTGGC
* * *
1071949 AGATAGCCTTTCTCGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
1 AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
*
1072014 TCGAAGGTCTTTTGTTGGT
66 TCGAAGGTCTTTTGTTGGC
*
1072033 AGATAGCCCTTCTTACCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
1 AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* *
1072098 TCGAAGGTCTTTTCTTAGC
66 TCGAAGGTCTTTTGTTGGC
* * * * *
1072117 AGATAGCCCTTCTTGCCTTGA-CATTTGTTGCAAATGATGTGCCTTTGAGCTGTGCGTAGTCGAA
1 AGATAGCCCTTCTTGCCTTGAGC-TATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
*
1072181 CTTGAAGGTCTTTTGTTGGC
65 CTCGAAGGTCTTTTGTTGGC
* * * * * *
1072201 AAATAGCCCTTCTTTCCGTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCAAAC
1 AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
1072266 TCGAAGGTCTTTTGTTGGC
66 TCGAAGGTCTTTTGTTGGC
* * *
1072285 AAATATCCCTTCTTGCCTTGAGCTATGTTGCA
1 AGATAGCCCTTCTTGCCTTGAGCTATGCTGCA
1072317 CACATGAACA
Statistics
Matches: 392, Mismatches: 52, Indels: 10
0.86 0.11 0.02
Matches are distributed among these distances:
81 71 0.18
83 1 0.00
84 319 0.81
85 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (84 bp):
AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
TCGAAGGTCTTTTGTTGGC
Found at i:1076097 original size:19 final size:20
Alignment explanation
Indices: 1076060--1076096 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
1076050 GCAAATGATA
1076060 AAAATAAAATGAAAGAAAAC
1 AAAATAAAATGAAAGAAAAC
1076080 AAAA-AAAATG-AAGAAAA
1 AAAATAAAATGAAAGAAAA
1076097 AAGTTAGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 6 0.35
20 4 0.24
ACGTcount: A:0.78, C:0.03, G:0.11, T:0.08
Consensus pattern (20 bp):
AAAATAAAATGAAAGAAAAC
Found at i:1077362 original size:24 final size:25
Alignment explanation
Indices: 1077335--1077383 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1077325 CAAGATAAAT
1077335 AAATAAAAA-TAAAGAAAATGTTAA
1 AAATAAAAATTAAAGAAAATGTTAA
*
1077359 AAATAAAAATTTAAGAAAATGTTAA
1 AAATAAAAATTAAAGAAAATGTTAA
1077384 TTTCTAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (25 bp):
AAATAAAAATTAAAGAAAATGTTAA
Found at i:1077430 original size:3 final size:3
Alignment explanation
Indices: 1077422--1077454 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1077412 TAAATTAGGA
1077422 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1077455 TTTTATTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1080822 original size:61 final size:61
Alignment explanation
Indices: 1080727--1080856 Score: 242
Period size: 61 Copynumber: 2.1 Consensus size: 61
1080717 TATGCACTGA
* *
1080727 AGTGCTAATACACATAAGGTCGTGCCCACCATATGCGCTAAGTGTCCTTTATATACACTAT
1 AGTGCTAATACACATAAGGTCGTGCCCACCATATGCACTAAGTGTACTTTATATACACTAT
1080788 AGTGCTAATACACATAAGGTCGTGCCCACCATATGCACTAAGTGTACTTTATATACACTAT
1 AGTGCTAATACACATAAGGTCGTGCCCACCATATGCACTAAGTGTACTTTATATACACTAT
1080849 AGTGCTAA
1 AGTGCTAA
1080857 ATCAAATATG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 67 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (61 bp):
AGTGCTAATACACATAAGGTCGTGCCCACCATATGCACTAAGTGTACTTTATATACACTAT
Found at i:1084311 original size:17 final size:16
Alignment explanation
Indices: 1084286--1084319 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1084276 TATTTTGTAA
*
1084286 TTAATTTATTTAAGTAT
1 TTAAATTATTTAA-TAT
1084303 TTAAATTATTTAATAT
1 TTAAATTATTTAATAT
1084319 T
1 T
1084320 GTATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTAAATTATTTAATAT
Found at i:1086105 original size:27 final size:27
Alignment explanation
Indices: 1086075--1086130 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
1086065 GAAGCCGCTG
*
1086075 CCGCCACCGTCACCTG-GTTTTATGACC
1 CCGCCACCGTCACC-GAGTTATATGACC
1086102 CCGCCACCGTCACCGAGTTATATGACC
1 CCGCCACCGTCACCGAGTTATATGACC
1086129 CC
1 CC
1086131 TATTGGAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.18, C:0.43, G:0.18, T:0.21
Consensus pattern (27 bp):
CCGCCACCGTCACCGAGTTATATGACC
Found at i:1089143 original size:2 final size:2
Alignment explanation
Indices: 1089136--1089172 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1089126 TACATATACA
1089136 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1089173 ATTGACGGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1090050 original size:19 final size:19
Alignment explanation
Indices: 1090023--1090074 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
1090013 TCGTTGATCG
* *
1090023 TTGATCGTTGACCGAGCAA
1 TTGACCGTTGACCAAGCAA
*
1090042 TTGACCGTTGACCAAGCAG
1 TTGACCGTTGACCAAGCAA
1090061 TTGACCGTTGACCA
1 TTGACCGTTGACCA
1090075 GCCGTTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (19 bp):
TTGACCGTTGACCAAGCAA
Found at i:1092995 original size:2 final size:2
Alignment explanation
Indices: 1092988--1093012 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1092978 GGGGGTTACA
1092988 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
1093013 ATTATATCTT
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:1093766 original size:2 final size:2
Alignment explanation
Indices: 1093759--1093828 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
1093749 GGGGGTTACA
1093759 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1093801 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
1093829 CTTTTTATTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1093899 original size:15 final size:14
Alignment explanation
Indices: 1093868--1093908 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
1093858 AGGTAAATGT
*
1093868 TTATCATTTTGACG
1 TTATCATTTTAACG
1093882 TTATCATTTTCAACG
1 TTATCATTTT-AACG
1093897 TTATCATTTTAA
1 TTATCATTTTAA
1093909 GTGTCTAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (14 bp):
TTATCATTTTAACG
Found at i:1095589 original size:57 final size:59
Alignment explanation
Indices: 1095481--1095614 Score: 168
Period size: 58 Copynumber: 2.3 Consensus size: 59
1095471 TTTATAAGGT
* *
1095481 AAAG-TACACAAATGGTCCCTCCAACTATAGGTATTGCTTTGTTGAGTCCTCTGACTA-TA
1 AAAGTTACA-AAATGGT-CCTCCAACTAAAGGTATTACTTTGTTGAGTCCTCTGACTATTA
* * *
1095540 AAAGTTATAAAATGGTCC-CCAACTACAAGGTTTTACTTT-TTTAGTCCTCTGACTATTA
1 AAAGTTACAAAATGGTCCTCCAACTA-AAGGTATTACTTTGTTGAGTCCTCTGACTATTA
1095598 AAAGTTACAAAATGGTC
1 AAAGTTACAAAATGGTC
1095615 ACTCGATTAT
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
57 22 0.33
58 30 0.45
59 11 0.17
60 3 0.05
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (59 bp):
AAAGTTACAAAATGGTCCTCCAACTAAAGGTATTACTTTGTTGAGTCCTCTGACTATTA
Found at i:1097232 original size:28 final size:29
Alignment explanation
Indices: 1097182--1097239 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
1097172 GATAAACTTT
* *
1097182 TATAAAAAATATATATTATTTATAGAAAA
1 TATAAAAAATATATATTAATTATAAAAAA
1097211 TATAAAAAA-ATAT-TTAAATTATAAAAAA
1 TATAAAAAATATATATT-AATTATAAAAAA
1097239 T
1 T
1097240 TTATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 2 0.08
28 15 0.58
29 9 0.35
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (29 bp):
TATAAAAAATATATATTAATTATAAAAAA
Found at i:1101075 original size:18 final size:19
Alignment explanation
Indices: 1101040--1101076 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1101030 CTAGGAATGT
1101040 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1101060 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1101077 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1104141 original size:2 final size:2
Alignment explanation
Indices: 1104082--1104125 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1104072 TCAAATTTTC
*
1104082 AT AT AT AT AT AT AT AT AT AG 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
1104124 AT
1 AT
1104126 TGAAGTTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1107368 original size:12 final size:11
Alignment explanation
Indices: 1107345--1107402 Score: 62
Period size: 11 Copynumber: 5.0 Consensus size: 11
1107335 TAAATGACTT
1107345 AAAAAAATAAA
1 AAAAAAATAAA
*
1107356 AAAAAGATAAA
1 AAAAAAATAAA
*
1107367 AAAAAAGATAAT
1 AAAAAA-ATAAA
*
1107379 AAACAAATAAA
1 AAAAAAATAAA
1107390 ATAAACAAATAAA
1 A-AAA-AAATAAA
1107403 CAAATTAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
11 20 0.53
12 11 0.29
13 7 0.18
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.12
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:1107377 original size:23 final size:22
Alignment explanation
Indices: 1107345--1107401 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
1107335 TAAATGACTT
1107345 AAAAAAATAA-AAAAAAGATAAA
1 AAAAAAATAATAAAAAA-ATAAA
*
1107367 AAAAAAGATAATAAACAAATAAA
1 AAAAAA-ATAATAAAAAAATAAA
1107390 ATAAACAAATAA
1 A-AAA-AAATAA
1107402 ACAAATTAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 6 0.20
23 10 0.33
24 12 0.40
25 2 0.07
ACGTcount: A:0.81, C:0.04, G:0.04, T:0.12
Consensus pattern (22 bp):
AAAAAAATAATAAAAAAATAAA
Found at i:1107394 original size:13 final size:13
Alignment explanation
Indices: 1107376--1107402 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1107366 AAAAAAAGAT
1107376 AATAAACAAATAA
1 AATAAACAAATAA
1107389 AATAAACAAATAA
1 AATAAACAAATAA
1107402 A
1 A
1107403 CAAATTAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (13 bp):
AATAAACAAATAA
Found at i:1107416 original size:21 final size:22
Alignment explanation
Indices: 1107376--1107421 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1107366 AAAAAAAGAT
1107376 AATAAACAAATAAAATAAA-CA
1 AATAAACAAATAAAATAAACCA
*
1107397 AATAAACAAATTAGAA-AAACCA
1 AATAAACAAA-TAAAATAAACCA
1107419 AAT
1 AAT
1107422 GAAAATGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.72, C:0.11, G:0.02, T:0.15
Consensus pattern (22 bp):
AATAAACAAATAAAATAAACCA
Found at i:1107862 original size:18 final size:17
Alignment explanation
Indices: 1107829--1107895 Score: 55
Period size: 18 Copynumber: 3.8 Consensus size: 17
1107819 TACATACATA
*
1107829 AATAAGTAAAAAAATAGT
1 AATAA-TAAAATAATAGT
1107847 AATAATAGAAATAATAAG-
1 AATAATA-AAATAAT-AGT
* * *
1107865 GATAATATAAAGAATAAT
1 AATAATA-AAATAATAGT
1107883 AATAATAAAATAA
1 AATAATAAAATAA
1107896 AAATGGTAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
17 8 0.21
18 29 0.74
19 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (17 bp):
AATAATAAAATAATAGT
Found at i:1107890 original size:21 final size:21
Alignment explanation
Indices: 1107847--1107896 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1107837 AAAAAATAGT
*
1107847 AATAATAGAAATAATAAGGATAA
1 AATAA-AG-AATAATAAGAATAA
* *
1107870 TATAAAGAATAATAATAATAA
1 AATAAAGAATAATAAGAATAA
1107891 AATAAA
1 AATAAA
1107897 AATGGTAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 17 0.74
22 2 0.09
23 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (21 bp):
AATAAAGAATAATAAGAATAA
Found at i:1107981 original size:25 final size:23
Alignment explanation
Indices: 1107936--1107981 Score: 74
Period size: 25 Copynumber: 1.9 Consensus size: 23
1107926 AAATATATAC
1107936 ATATATAATATAATATAATAACA
1 ATATATAATATAATATAATAACA
1107959 ATATATATATATATATATAATAA
1 ATATATA-ATATA-ATATAATAA
1107982 AACGTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 7 0.33
24 5 0.24
25 9 0.43
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
ATATATAATATAATATAATAACA
Found at i:1109617 original size:106 final size:105
Alignment explanation
Indices: 1109485--1110253 Score: 1277
Period size: 106 Copynumber: 7.3 Consensus size: 105
1109475 CTGTCTTGAG
** * *
1109485 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGGTTGGGAAGTTATTTATTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-TTGTTTATTGACAACCAGCGGTCC
1109550 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
* *
1109591 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-TTGTTTATTGACAACCAGCGGTCC
*
1109656 CTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATA
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
* * * *
1109697 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGGAATTGAGAAGTTATTTGTTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-TTGTTTATTGACAACCAGCGGTCC
*
1109762 CTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
* * *
1109803 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTGTTTATTGACAACCAGCGGTCCC
*
1109868 TTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
* *
1109908 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTGTTTATTGACAACCAGCGGTCCC
1109973 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
* *
1110013 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTAACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AATTGTTTATTGACAACCAGCGGTCC
*
1110078 CTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
* *
1110119 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCGGCGGTCCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTGTTTATTGACAACCAGCGGTCCC
*
1110184 TTCGTCGTGAAGTGGAACTTGCGTTGTCTGGAGTCCAATA
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
1110224 TCCTTCGTTATGAAGTTGAAATTGGCTCTG
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1110254 GGTAAAACCT
Statistics
Matches: 630, Mismatches: 32, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
105 290 0.46
106 340 0.54
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATTGTTTATTGACAACCAGCGGTCCC
TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
Found at i:1110070 original size:211 final size:212
Alignment explanation
Indices: 1109485--1110253 Score: 1301
Period size: 211 Copynumber: 3.6 Consensus size: 212
1109475 CTGTCTTGAG
** * *
1109485 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGGTTGGGAAGTTATTTATTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGATATTTATTGACAACCAGCGGTCC
1109550 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
* *
1109615 GCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCG
131 GCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
1109680 TTGTCTGGAGTCCAATA
196 TTGTCTGGAGTCCAATA
* * * *
1109697 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGGAATTGAGAAGTTATTTGTTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGATATTTATTGACAACCAGCGGTCC
*
1109762 CTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
* * *
1109827 GCTCTGAAATTGGGAAA-TGTTTATTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCG
131 GCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
1109891 TTGTCTGGAGTCCAATA
196 TTGTCTGGAGTCCAATA
* *
1109908 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGATATTTATTGACAACCAGCGGTCC
*
1109972 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
* *
1110037 GCTCTGAAATTGAGAAATTGTTTGTTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACG
131 GCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
1110102 TTGTCTGGAGTCCAATA
196 TTGTCTGGAGTCCAATA
* *
1110119 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTATTGACAACCGGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGATATTTATTGACAACCAGCGGTCC
* * *
1110183 CTTCGTCGTGAAGTGGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTATGAAGTTGAAATTG
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
1110248 GCTCTG
131 GCTCTG
1110254 GGTAAAACCT
Statistics
Matches: 527, Mismatches: 29, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
210 100 0.19
211 289 0.55
212 138 0.26
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (212 bp):
TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGATATTTATTGACAACCAGCGGTCC
CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
GCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
TTGTCTGGAGTCCAATA
Found at i:1110070 original size:316 final size:317
Alignment explanation
Indices: 1109485--1110253 Score: 1324
Period size: 316 Copynumber: 2.4 Consensus size: 317
1109475 CTGTCTTGAG
** * *
1109485 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGGTTGGGAAGTTATTTATTGACAACCAGCGGTCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGACAACCAGCGGTCC
*
1109550 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
* *
1109615 GCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCG
130 GCTCTGAAATTGAGAAGATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCG
* *
1109680 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGGAATTGAGAAGTTATTTG
195 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTG
* *
1109745 TTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
260 TTAACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
*
1109803 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCC
*
1109868 TTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
* *
1109933 CTCTGAAATTGGGAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
131 CTCTGAAATTGAGAAGATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGT
* *
1109997 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGT
196 TGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTGT
*
1110062 TAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
261 TAACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
* *
1110119 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCGGCGGTCCC
1 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCC
* *
1110184 TTCGTCGTGAAGTGGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTATGAAGTTGAAATTGG
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
1110249 CTCTG
131 CTCTG
1110254 GGTAAAACCT
Statistics
Matches: 427, Mismatches: 24, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
316 290 0.68
317 100 0.23
318 37 0.09
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (317 bp):
TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCC
TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
CTCTGAAATTGAGAAGATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGT
TGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTGT
TAACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATA
Found at i:1111105 original size:50 final size:52
Alignment explanation
Indices: 1111027--1111124 Score: 146
Period size: 50 Copynumber: 1.9 Consensus size: 52
1111017 CTTTTTTTCC
* * *
1111027 TCTTTTTCTTTTTTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAACGT
1 TCTTTTTCTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACGT
*
1111079 TCTTTTT-TTTTTT-AACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 TCTTTTTCTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAA
1111125 GCGAAGTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 29 0.69
51 6 0.14
52 7 0.17
ACGTcount: A:0.14, C:0.24, G:0.14, T:0.47
Consensus pattern (52 bp):
TCTTTTTCTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACGT
Found at i:1121529 original size:21 final size:20
Alignment explanation
Indices: 1121505--1121575 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 20
1121495 ATAAATGACT
1121505 TAAAAAAATAAATAAAAAAGA
1 TAAAAAAATAAATAAAAAA-A
* *
1121526 TAAAAAAA-ATAATAAGATAA
1 TAAAAAAATA-AATAAAAAAA
* *
1121546 TAAACAAATAAAATAAACAAA
1 TAAAAAAAT-AAATAAAAAAA
*
1121567 TAAACAAAT
1 TAAAAAAAT
1121576 TAGAAAAACC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
20 9 0.22
21 31 0.76
22 1 0.02
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.17
Consensus pattern (20 bp):
TAAAAAAATAAATAAAAAAA
Found at i:1121563 original size:13 final size:13
Alignment explanation
Indices: 1121544--1121570 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1121534 ATAATAAGAT
1121544 AATAAACAAATAA
1 AATAAACAAATAA
1121557 AATAAACAAATAA
1 AATAAACAAATAA
1121570 A
1 A
1121571 CAAATTAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (13 bp):
AATAAACAAATAA
Found at i:1121584 original size:21 final size:22
Alignment explanation
Indices: 1121544--1121589 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1121534 ATAATAAGAT
1121544 AATAAACAAATAAAATAAA-CA
1 AATAAACAAATAAAATAAACCA
*
1121565 AATAAACAAATTAGAA-AAACCA
1 AATAAACAAA-TAAAATAAACCA
1121587 AAT
1 AAT
1121590 GAAAATGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.72, C:0.11, G:0.02, T:0.15
Consensus pattern (22 bp):
AATAAACAAATAAAATAAACCA
Found at i:1122057 original size:18 final size:18
Alignment explanation
Indices: 1122035--1122084 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
1122025 AAAAAATAGT
*
1122035 AATAATAGAAATAATAAG
1 AATAATAAAAATAATAAG
* * * *
1122053 GATAATATAAAGAATAAT
1 AATAATAAAAATAATAAG
1122071 AATAATAAAAATAA
1 AATAATAAAAATAA
1122085 AATGGTAAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (18 bp):
AATAATAAAAATAATAAG
Found at i:1122138 original size:29 final size:26
Alignment explanation
Indices: 1122105--1122168 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 26
1122095 TATAAAAAGA
1122105 AATAAGTAAATATACATATATATACATAT
1 AATAA-TAAATA-ACATATA-ATACATAT
*
1122134 AATAAT-AATAACATATAATATATAT
1 AATAATAAATAACATATAATACATAT
1122159 ATATAATAAA
1 A-ATAATAAA
1122169 CGTAATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 8 0.25
26 12 0.38
27 6 0.19
28 1 0.03
29 5 0.16
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (26 bp):
AATAATAAATAACATATAATACATAT
Found at i:1122153 original size:13 final size:14
Alignment explanation
Indices: 1122114--1122167 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 14
1122104 AAATAAGTAA
1122114 ATATACATATATATAC
1 ATATA-ATA-ATATAC
1122130 ATATAATAATAATAAC
1 ATATAATAAT-AT-AC
*
1122146 ATATAAT-ATATAT
1 ATATAATAATATAC
1122159 ATATAATAA
1 ATATAATAA
1122168 ACGTAATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
13 8 0.24
14 5 0.15
15 7 0.21
16 14 0.41
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
ATATAATAATATAC
Found at i:1132070 original size:18 final size:19
Alignment explanation
Indices: 1132033--1132070 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1132023 TTTATGGGCT
*
1132033 ATGTGCATCGATGACATCA
1 ATGTGCACCGATGACATCA
1132052 ATGTGCACCGATG-CATCA
1 ATGTGCACCGATGACATCA
1132070 A
1 A
1132071 GGATAAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (19 bp):
ATGTGCACCGATGACATCA
Found at i:1132870 original size:23 final size:23
Alignment explanation
Indices: 1132836--1132904 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
1132826 CATTATTATA
1132836 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
1132859 TGGCACTCCGGTGTAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
1132882 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
1132905 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.29
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:1147272 original size:18 final size:18
Alignment explanation
Indices: 1147249--1147289 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1147239 TCGGGTTTCA
1147249 TCTCCCGATCTTCGTCGT
1 TCTCCCGATCTTCGTCGT
1147267 TCTCCCGATCTTCGTCGT
1 TCTCCCGATCTTCGTCGT
1147285 TCTCC
1 TCTCC
1147290 GTTAGATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.05, C:0.41, G:0.15, T:0.39
Consensus pattern (18 bp):
TCTCCCGATCTTCGTCGT
Found at i:1150257 original size:70 final size:70
Alignment explanation
Indices: 1150174--1150314 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
1150164 ACTGAAGGTA
1150174 TTTTCGAAATGTGTTGTGCTTTACTTCGATTGATATAAGCTCTTTGTTCCTATGTAACTTAAGAG
1 TTTTCGAAATGTGTTGTGCTTTACTTCGATTGATATAAGCTCTTTGTTCCTATGTAACTTAAGAG
1150239 AATTT
66 AATTT
1150244 TTTTCGAAATGTGTTGTGCTTTACTTCGATTGATATAAGCTCTTTGTTCCTATGTAACTTAAGAG
1 TTTTCGAAATGTGTTGTGCTTTACTTCGATTGATATAAGCTCTTTGTTCCTATGTAACTTAAGAG
1150309 AATTT
66 AATTT
1150314 T
1 T
1150315 CTATTACAGC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (70 bp):
TTTTCGAAATGTGTTGTGCTTTACTTCGATTGATATAAGCTCTTTGTTCCTATGTAACTTAAGAG
AATTT
Found at i:1153578 original size:20 final size:20
Alignment explanation
Indices: 1153550--1153593 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1153540 AAATGAATTT
*
1153550 ATTTAGTGACCAAATTATAA
1 ATTTAGTGACCAAAGTATAA
*
1153570 ATTTGGTGACCAAAGTATAA
1 ATTTAGTGACCAAAGTATAA
1153590 ATTT
1 ATTT
1153594 TGAAAAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (20 bp):
ATTTAGTGACCAAAGTATAA
Found at i:1155774 original size:44 final size:45
Alignment explanation
Indices: 1155693--1155829 Score: 206
Period size: 45 Copynumber: 3.0 Consensus size: 45
1155683 GATAAACAAA
1155693 AAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGAT
1 AAAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAGTATATTGAT
*
1155739 AAAATAAGCTT-CAAGCTTATGGGATAAATGGTAAGTATACTTG-T
1 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATA-TTGAT
* * *
1155783 AAAATAAGCTTACGAGCTTATGGGATAAATGATAAATATATTAAT
1 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGAT
1155828 AA
1 AA
1155830 GAAATTTTAT
Statistics
Matches: 83, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
44 29 0.35
45 43 0.52
46 11 0.13
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.31
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGAT
Found at i:1160423 original size:18 final size:18
Alignment explanation
Indices: 1160400--1160452 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
1160390 CCAGCTCTTG
*
1160400 GATGAAGAAGAAGATGAT
1 GATGAAGAAGAAGAAGAT
1160418 GATGAAGAAGAAGAAGAT
1 GATGAAGAAGAAGAAGAT
*
1160436 GATGATGAAGAAGAAGA
1 GATGAAGAAGAAGAAGA
1160453 AACACATGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.53, C:0.00, G:0.34, T:0.13
Consensus pattern (18 bp):
GATGAAGAAGAAGAAGAT
Found at i:1160424 original size:15 final size:15
Alignment explanation
Indices: 1160400--1160453 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
1160390 CCAGCTCTTG
1160400 GATGAAGAAGAAGAT
1 GATGAAGAAGAAGAT
*
1160415 GATGATGAAGAAGA-
1 GATGAAGAAGAAGAT
* *
1160429 -A-GAAGATGATGAT
1 GATGAAGAAGAAGAT
*
1160442 GAAGAAGAAGAA
1 GATGAAGAAGAA
1160454 ACACATGGGT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
12 8 0.27
13 1 0.03
14 1 0.03
15 20 0.67
ACGTcount: A:0.54, C:0.00, G:0.33, T:0.13
Consensus pattern (15 bp):
GATGAAGAAGAAGAT
Found at i:1160429 original size:21 final size:21
Alignment explanation
Indices: 1160403--1160453 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
1160393 GCTCTTGGAT
1160403 GAAGAAGAAGATGATGATGAA
1 GAAGAAGAAGATGATGATGAA
1160424 GAAGAAGAAGATGATGATGAA
1 GAAGAAGAAGATGATGATGAA
1160445 GAAGAAGAA
1 GAAGAAGAA
1160454 ACACATGGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.55, C:0.00, G:0.33, T:0.12
Consensus pattern (21 bp):
GAAGAAGAAGATGATGATGAA
Found at i:1162075 original size:67 final size:67
Alignment explanation
Indices: 1161992--1162121 Score: 181
Period size: 67 Copynumber: 1.9 Consensus size: 67
1161982 TTGTTACTTG
*
1161992 TTAAGCTCGTTAAAATTTTGAC-CGATTAGTGCTCCTTAAGAAAATTTATTGCTCGACTAGTTGA
1 TTAAGCTCGTTAAAATTTT-ACTCGATTAGTGCTCATTAAGAAAATTTATTGCTCGACTAGTTGA
1162056 TTT
65 TTT
* * * * * *
1162059 TTAAGTTCTTTAAAATTTTTCTCGATTGGTGCTCATTAAGAAAATTTGTTGCTCGACTGGTTG
1 TTAAGCTCGTTAAAATTTTACTCGATTAGTGCTCATTAAGAAAATTTATTGCTCGACTAGTTG
1162122 CTCGTTAAGC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 1 0.02
67 54 0.98
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (67 bp):
TTAAGCTCGTTAAAATTTTACTCGATTAGTGCTCATTAAGAAAATTTATTGCTCGACTAGTTGAT
TT
Found at i:1162130 original size:32 final size:29
Alignment explanation
Indices: 1162070--1162130 Score: 77
Period size: 32 Copynumber: 2.0 Consensus size: 29
1162060 TAAGTTCTTT
*
1162070 AAAATTTTTCTCGATTGGTGCTCATTAAG
1 AAAATTTTTCTCGACTGGTGCTCATTAAG
*
1162099 AAAATTTGTTGCTCGACTGGTTGCTCGTTAAG
1 AAAATTT-TT-CTCGACTGG-TGCTCATTAAG
1162131 CTCACCAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 7 0.26
30 2 0.07
31 8 0.30
32 10 0.37
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (29 bp):
AAAATTTTTCTCGACTGGTGCTCATTAAG
Found at i:1162143 original size:67 final size:67
Alignment explanation
Indices: 1162014--1162145 Score: 156
Period size: 67 Copynumber: 2.0 Consensus size: 67
1162004 AAATTTTGAC
* ** * ***
1162014 CGATTAGTGCTCCTTAAGAAAATTTATTGCTCGACTAGTTGATTTTTAAGTTCTTTAAAATTTTT
1 CGATTAGTGCTCATTAAGAAAATTTATTGCTCGACTAGTTGATCGTTAAGCTCACCAAAATTTTT
1162079 CT
66 CT
* * * * *
1162081 CGATTGGTGCTCATTAAGAAAATTTGTTGCTCGACTGGTTGCTCGTTAAGCTCACCAGAATTTTT
1 CGATTAGTGCTCATTAAGAAAATTTATTGCTCGACTAGTTGATCGTTAAGCTCACCAAAATTTTT
1162146 TATTTTTTAA
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
67 53 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (67 bp):
CGATTAGTGCTCATTAAGAAAATTTATTGCTCGACTAGTTGATCGTTAAGCTCACCAAAATTTTT
CT
Found at i:1164463 original size:25 final size:25
Alignment explanation
Indices: 1164413--1164463 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
1164403 CGTTATTTAT
* *
1164413 AATAAATAAATCATATCGACATAAA
1 AATAAATAAATCATATCCACAGAAA
*
1164438 AATAAATAAAT-ATTTCTCACAGAAA
1 AATAAATAAATCATATC-CACAGAAA
1164463 A
1 A
1164464 TAATTTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.59, C:0.12, G:0.04, T:0.25
Consensus pattern (25 bp):
AATAAATAAATCATATCCACAGAAA
Found at i:1165695 original size:13 final size:13
Alignment explanation
Indices: 1165677--1165703 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1165667 TTACAGAAGC
1165677 GCATATGAAGACT
1 GCATATGAAGACT
1165690 GCATATGAAGACT
1 GCATATGAAGACT
1165703 G
1 G
1165704 TTCAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:1166188 original size:20 final size:20
Alignment explanation
Indices: 1166165--1166205 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1166155 CATATTTCTC
1166165 ACCAAGCCACTCAATTTCAT
1 ACCAAGCCACTCAATTTCAT
1166185 ACCAAGCCACTCAATTTCAT
1 ACCAAGCCACTCAATTTCAT
1166205 A
1 A
1166206 AACCTTACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.34, G:0.05, T:0.24
Consensus pattern (20 bp):
ACCAAGCCACTCAATTTCAT
Found at i:1167902 original size:59 final size:58
Alignment explanation
Indices: 1167836--1167998 Score: 193
Period size: 59 Copynumber: 2.8 Consensus size: 58
1167826 TATGACCCTC
* * *
1167836 ATTATAAAGTGGTCCTTAAACTTTTGAATATTCCAATTTCATCCCAAACTATGACTTTT
1 ATTATAAATTGTTCCTTAAACTTTTGAATATTCCAATTTCATCCCAAACTATGAC-ATT
* * *
1167895 ATTATAAATTTTTCCTTAAAATTTTGAATA-TCCAATATCATCCCCAAACTATGACATT
1 ATTATAAATTGTTCCTTAAACTTTTGAATATTCCAATTTCAT-CCCAAACTATGACATT
* ** * * *
1167953 ATTCTAAATTGTTCCCCAAACTTTTGAATATTTCACTTTTATCCCA
1 ATTATAAATTGTTCCTTAAACTTTTGAATATTCCAATTTCATCCCA
1167999 GACATCCAAA
Statistics
Matches: 87, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
58 41 0.47
59 46 0.53
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (58 bp):
ATTATAAATTGTTCCTTAAACTTTTGAATATTCCAATTTCATCCCAAACTATGACATT
Done.