Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold409
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: 3905031
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 8 of 25
Found at i:1128900 original size:13 final size:13
Alignment explanation
Indices: 1128882--1128919 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1128872 ATAATCCCCC
1128882 TGTATCGATACAG
1 TGTATCGATACAG
*
1128895 TGTATCGATACAT
1 TGTATCGATACAG
1128908 TGTATCGATACA
1 TGTATCGATACA
1128920 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1131020 original size:15 final size:15
Alignment explanation
Indices: 1131000--1131030 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1130990 ATTTCGTTTG
*
1131000 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1131015 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1131030 G
1 G
1131031 GATATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1131101 original size:21 final size:21
Alignment explanation
Indices: 1131077--1131145 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
1131067 TAGATTTTCT
1131077 TCAAAAATCTCTACATCATTG
1 TCAAAAATCTCTACATCATTG
* * * * *
1131098 TCAACAATTGTTCTAGAT-TTTCT
1 TCAA-AAAT-CTCTACATCATT-G
1131121 TCAAAAATCTCTACATCATTG
1 TCAAAAATCTCTACATCATTG
1131142 TCAA
1 TCAA
1131146 CAAAAGATAC
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
21 14 0.41
22 10 0.29
23 10 0.29
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.38
Consensus pattern (21 bp):
TCAAAAATCTCTACATCATTG
Found at i:1131111 original size:44 final size:44
Alignment explanation
Indices: 1131061--1131148 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
1131051 TGTGTGATGC
1131061 TTGTTCTAGATTTTCTTCAAAAATCTCTACATCATTGTCAACAA
1 TTGTTCTAGATTTTCTTCAAAAATCTCTACATCATTGTCAACAA
1131105 TTGTTCTAGATTTTCTTCAAAAATCTCTACATCATTGTCAACAA
1 TTGTTCTAGATTTTCTTCAAAAATCTCTACATCATTGTCAACAA
1131149 AAGATACCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (44 bp):
TTGTTCTAGATTTTCTTCAAAAATCTCTACATCATTGTCAACAA
Found at i:1132906 original size:21 final size:21
Alignment explanation
Indices: 1132877--1132921 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1132867 AAGTTTTTAT
*
1132877 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1132897 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1132919 TTT
1 TTT
1132922 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1135123 original size:13 final size:13
Alignment explanation
Indices: 1135105--1135130 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1135095 ATATTTTTTG
1135105 TGTATCGATACAT
1 TGTATCGATACAT
1135118 TGTATCGATACAT
1 TGTATCGATACAT
1135131 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1135141 original size:32 final size:33
Alignment explanation
Indices: 1135084--1135148 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
1135074 TACAAGCCAA
1135084 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
1135118 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
1135149 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:1135142 original size:19 final size:19
Alignment explanation
Indices: 1135084--1135148 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
1135074 TACAAGCCAA
1135084 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
1135105 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
1135118 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
1135137 TGTATCGATACA
1 TGTATCGATACA
1135149 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:1138557 original size:16 final size:16
Alignment explanation
Indices: 1138513--1138589 Score: 64
Period size: 16 Copynumber: 4.8 Consensus size: 16
1138503 GTTACGTTAT
*
1138513 TTCGAGTTATTTTTGGG
1 TTCGGGTTA-TTTTGGG
**
1138530 TTCGGGACATTTTGGG
1 TTCGGGTTATTTTGGG
* **
1138546 TTTGGGTTATTTCAGG
1 TTCGGGTTATTTTGGG
* *
1138562 TTTGGGTTGTTTTGGG
1 TTCGGGTTATTTTGGG
*
1138578 TTCGGGTCATTT
1 TTCGGGTTATTT
1138590 CAAGTTCGAG
Statistics
Matches: 46, Mismatches: 14, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
16 40 0.87
17 6 0.13
ACGTcount: A:0.09, C:0.08, G:0.34, T:0.49
Consensus pattern (16 bp):
TTCGGGTTATTTTGGG
Found at i:1139614 original size:16 final size:16
Alignment explanation
Indices: 1139595--1139640 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
1139585 TCGAGTTCGA
1139595 GTCATTTTGGATTCAG
1 GTCATTTTGGATTCAG
1139611 GTCATTTTGGATTCAG
1 GTCATTTTGGATTCAG
*
1139627 GTCATTTCGGATTC
1 GTCATTTTGGATTC
1139641 GGGTTGTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.17, C:0.15, G:0.24, T:0.43
Consensus pattern (16 bp):
GTCATTTTGGATTCAG
Found at i:1143072 original size:19 final size:19
Alignment explanation
Indices: 1143026--1143081 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1143016 CTACCAATTT
*
1143026 CATGTATCGATACATTTGAG
1 CATGTATCGATACA-ATGAG
*
1143046 TATGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
*
1143065 CATTTATCGATACAATG
1 CATGTATCGATACAATG
1143082 TATCAATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 19 0.59
20 13 0.41
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:1143299 original size:117 final size:117
Alignment explanation
Indices: 1143158--1143392 Score: 470
Period size: 117 Copynumber: 2.0 Consensus size: 117
1143148 TTGTAGCCTA
1143158 AGTCAACCTTAATATATCGATATAAATACCTATATATCGATACTTTGGTATATTTTTACTTGAAA
1 AGTCAACCTTAATATATCGATATAAATACCTATATATCGATACTTTGGTATATTTTTACTTGAAA
1143223 ACATTCGATTTAAGGCTTGAAAACACTTATATGAAACTCTAAAATATTATTG
66 ACATTCGATTTAAGGCTTGAAAACACTTATATGAAACTCTAAAATATTATTG
1143275 AGTCAACCTTAATATATCGATATAAATACCTATATATCGATACTTTGGTATATTTTTACTTGAAA
1 AGTCAACCTTAATATATCGATATAAATACCTATATATCGATACTTTGGTATATTTTTACTTGAAA
1143340 ACATTCGATTTAAGGCTTGAAAACACTTATATGAAACTCTAAAATATTATTG
66 ACATTCGATTTAAGGCTTGAAAACACTTATATGAAACTCTAAAATATTATTG
1143392 A
1 A
1143393 TATTGAAAAT
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 118 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (117 bp):
AGTCAACCTTAATATATCGATATAAATACCTATATATCGATACTTTGGTATATTTTTACTTGAAA
ACATTCGATTTAAGGCTTGAAAACACTTATATGAAACTCTAAAATATTATTG
Found at i:1144070 original size:165 final size:163
Alignment explanation
Indices: 1143676--1144100 Score: 425
Period size: 165 Copynumber: 2.6 Consensus size: 163
1143666 TTTCATCAGC
* *
1143676 TTAAAATTTTTAAAATTCATTAAATATTATCACTAAACTCCCATTAAATCAATTTTGAAAAATCC
1 TTAAAATTTTT-AAATTCATT-AATATTGTCATTAAACTCCCATTAAATCAATTTTG-AAAAT--
* * * * *
1143741 CTT-TTTA-TTTCATGAGTTTTTTATTTTTTTCCTTAAAATACCTTTATTTCCTAAAAACTAAAT
61 TTTATTTATTTTCATGAGTTTTTCATTTTTTTCCTTAAAATACC-TCATTTCCGAAAAACCAAAT
*
1143804 TTTCTATTCTATAAAGGTTTTCGGGAAGATTTTTCTCGAT
125 TTTCTATTCCATAAAGGTTTTCGGG-AGATTTTTCTCGAT
* * *
1143844 TTAAAATTTTTAGAATTCATTTAATATTGTCATTAAGCCCCCATTAAATCAGTTTTGAAAATTTT
1 TTAAAATTTTTA-AATTCA-TTAATATTGTCATTAAACTCCCATTAAATCAATTTTGAAAATTTT
* * * *
1143909 ATTTATTTTTATGAGTTTTTCATTTTTTT-CTTGAAATGTCC-CATTTTCGAAAAACCAAATTTT
64 ATTTATTTTCATGAGTTTTTCATTTTTTTCCTTAAAAT-ACCTCATTTCCGAAAAACCAAATTTT
* * * * *
1143972 TTATTCCATAAATGTTTTTGAGG-GTATTTTTCTTGGT
128 CTATTCCATAAAGGTTTTCG-GGAG-ATTTTTCTCGAT
* *
1144009 TTAAAATTTTTCAAATTCATCTAATATTGTCATTAAATTCACATTAAA-CTAATTTTGAAAATTT
1 TTAAAATTTTT-AAATTCAT-TAATATTGTCATTAAACTCCCATTAAATC-AATTTTGAAAATTT
* * * *
1144073 AAATTA-TTTCATGA-ATTTTGATTTTTTT
63 TATTTATTTTCATGAGTTTTTCATTTTTTT
1144101 TATATAATGA
Statistics
Matches: 217, Mismatches: 30, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
163 12 0.06
164 10 0.05
165 103 0.47
166 14 0.06
167 29 0.13
168 47 0.22
169 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.48
Consensus pattern (163 bp):
TTAAAATTTTTAAATTCATTAATATTGTCATTAAACTCCCATTAAATCAATTTTGAAAATTTTAT
TTATTTTCATGAGTTTTTCATTTTTTTCCTTAAAATACCTCATTTCCGAAAAACCAAATTTTCTA
TTCCATAAAGGTTTTCGGGAGATTTTTCTCGAT
Found at i:1145766 original size:144 final size:139
Alignment explanation
Indices: 1145535--1145906 Score: 403
Period size: 144 Copynumber: 2.6 Consensus size: 139
1145525 ATTTTATGAA
* * *
1145535 ATTTCTAAT-ATTTTCATGGTTATCTGTAGGGGTA-TGAAAATTTTTAAAACTTTTCGTATCTTT
1 ATTTCTAATAATTCT-ATGGTTTTCCGTAGGGGTATTG-AAA--TTTAAAACTTTTCGTATCTTT
* * * * *
1145598 TTGGTTCTCTATTAAAGTACGAAATGAATTTTTTTTTATAATTCAAAAATTAAATAAAAATTATT
62 TCGGTTCTCCATTAAGGTATGAAATGAA-TTTTTTTTAAAATT-AAAAATTAAATAAAAATTATT
1145663 ATCTCAAATTTTCT-AG
125 ATCT-AAATTTT-TAAG
*
1145679 ATTTCTAATAATTCTATGGTTTTCCGTAGGGGTATTGAAATCTTCAAAACTTTTGGTATCTTTTC
1 ATTTCTAATAATTCTATGGTTTTCCGTAGGGGTATTGAAAT-TT-AAAACTTTTCGTATCTTTTC
*
1145744 GGTTCTCCATTAAGGTATGAAATGAATTTTTTTTAAAATTAAAATTTAAATAAAAATTATTATCT
64 GGTTCTCCATTAAGGTATGAAATGAATTTTTTTTAAAATTAAAAATTAAATAAAAATTATTATCT
*
1145809 TAATTTTTAAG
129 AAATTTTTAAG
* * * * ** *
1145820 ACTTCT-ATCATTTCTATGGGTGTT-CGTAGAGGTATAAAAATTTACAAACTTTTCGTATCCTTT
1 ATTTCTAAT-AATTCTAT-GGTTTTCCGTAGGGGTATTGAAATTTA-AAACTTTTCGTATCTTTT
** *
1145883 CGGTTCTCCAAGACGGTATGAAAT
63 CGGTTCTCCATTAAGGTATGAAAT
1145907 TTATTTTTGC
Statistics
Matches: 198, Mismatches: 22, Indels: 20
0.82 0.09 0.08
Matches are distributed among these distances:
139 1 0.01
140 42 0.21
141 34 0.17
142 30 0.15
143 15 0.08
144 70 0.35
145 6 0.03
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (139 bp):
ATTTCTAATAATTCTATGGTTTTCCGTAGGGGTATTGAAATTTAAAACTTTTCGTATCTTTTCGG
TTCTCCATTAAGGTATGAAATGAATTTTTTTTAAAATTAAAAATTAAATAAAAATTATTATCTAA
ATTTTTAAG
Found at i:1145906 original size:140 final size:143
Alignment explanation
Indices: 1145577--1145906 Score: 397
Period size: 140 Copynumber: 2.3 Consensus size: 143
1145567 TATGAAAATT
* * * * *
1145577 TTTA-AAACTTTTCGTATCTTTTTGGTTCTCTATTAAAGTACGAAATGAATTTTTTTTTATAATT
1 TTTACAAACTTTTCGTATCTTTTCGGTTCTCCATTAAGGTATGAAATGAATTTTTTTTTAAAATT
* *
1145641 CAAAAATTAAATAAAAATTATTATCTCAAATTTTCTAGATTTCTAATAATTCTATGGTTTTCCGT
66 CAAAAATTAAATAAAAATTATTATCTCAAATTTTCTAGACTTCTAATAATTCTATGGTGTTCCGT
* **
1145706 AGGGGTATTGAAA
131 AGAGGTATAAAAA
*
1145719 TCTT-CAAAACTTTTGGTATCTTTTCGGTTCTCCATTAAGGTATGAAATGAA-TTTTTTTTAAAA
1 T-TTAC-AAACTTTTCGTATCTTTTCGGTTCTCCATTAAGGTATGAAATGAATTTTTTTTTAAAA
* * *
1145782 TT-AAAATTTAAATAAAAATTATTATCT-TAATTTT-TAAGACTTCT-ATCATTTCTATGGGTGT
64 TTCAAAAATTAAATAAAAATTATTATCTCAAATTTTCT-AGACTTCTAAT-AATTCTAT-GGTGT
1145843 T-CGTAGAGGTATAAAAA
126 TCCGTAGAGGTATAAAAA
* ** *
1145860 TTTACAAACTTTTCGTATCCTTTCGGTTCTCCAAGACGGTATGAAAT
1 TTTACAAACTTTTCGTATCTTTTCGGTTCTCCATTAAGGTATGAAAT
1145907 TTATTTTTGC
Statistics
Matches: 162, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
140 42 0.26
141 35 0.22
142 30 0.19
143 15 0.09
144 40 0.25
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (143 bp):
TTTACAAACTTTTCGTATCTTTTCGGTTCTCCATTAAGGTATGAAATGAATTTTTTTTTAAAATT
CAAAAATTAAATAAAAATTATTATCTCAAATTTTCTAGACTTCTAATAATTCTATGGTGTTCCGT
AGAGGTATAAAAA
Found at i:1153824 original size:47 final size:47
Alignment explanation
Indices: 1153708--1153827 Score: 143
Period size: 47 Copynumber: 2.6 Consensus size: 47
1153698 CGTTTGGTTA
* * * *
1153708 TATTGGCATTAGAAC-CTAGTCAAACTTTTTCTGCCCTTGTTTGACTG
1 TATTGGCATTAGGACTC-AGTCAAACTCTTTCTACCCTTCTTTGACTG
** **
1153755 TATTGGCATTAGGGTTTGGTCAAACTCTTTCTACCCTTCTTTGACTG
1 TATTGGCATTAGGACTCAGTCAAACTCTTTCTACCCTTCTTTGACTG
*
1153802 TATTGGCCTTAGGACTCAGTCAAACT
1 TATTGGCATTAGGACTCAGTCAAACT
1153828 ATTTTTCTTC
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (47 bp):
TATTGGCATTAGGACTCAGTCAAACTCTTTCTACCCTTCTTTGACTG
Found at i:1154079 original size:41 final size:40
Alignment explanation
Indices: 1153976--1154089 Score: 93
Period size: 41 Copynumber: 2.8 Consensus size: 40
1153966 GTCATTTTCG
* **
1153976 ATTGGCTTTATTGGTTTCACCCTAGCCAACCTTCTAATTT
1 ATTGGCTTTATTGGTTTCACCCTGGCCAACCTTCTAACCT
* * *** * ** *
1154016 GTTGACTTTATCAATTTTACCCTGGTTAACCCTTCTTACCT
1 ATTGGCTTTATTGGTTTCACCCTGGCCAA-CCTTCTAACCT
* *
1154057 ATTGGCTTTATTGGTTTCACCCTGTCTAACCTT
1 ATTGGCTTTATTGGTTTCACCCTGGCCAACCTT
1154090 TTAATTGGTC
Statistics
Matches: 53, Mismatches: 20, Indels: 2
0.71 0.27 0.03
Matches are distributed among these distances:
40 24 0.45
41 29 0.55
ACGTcount: A:0.18, C:0.25, G:0.12, T:0.44
Consensus pattern (40 bp):
ATTGGCTTTATTGGTTTCACCCTGGCCAACCTTCTAACCT
Found at i:1154282 original size:85 final size:85
Alignment explanation
Indices: 1154100--1154357 Score: 299
Period size: 85 Copynumber: 3.0 Consensus size: 85
1154090 TTAATTGGTC
* **
1154100 GACTTGTCAGTTCATTCCTAA-TCAACCTTTTTATCCTTTGTTTACTTGTCAACTTAGTC-CAGG
1 GACTTGTCAGTTCATTCC-AAGTCAACCTTTTTATCCTTTGTTTACATGTTGACTTAGTCTCAGG
* *
1154163 TAAATCCTTTCAGCCTTTGTT
65 TAAATCCTTTCATCTTTTGTT
* * * *
1154184 GACTTGTCTGTTCAATT-CAAGTCAACCATTTTATCCTTTGTTTACATGTTGACTTAATCTCGGG
1 GACTTGTCAGTTC-ATTCCAAGTCAACCTTTTTATCCTTTGTTTACATGTTGACTTAGTCTCAGG
1154248 TAAATCCTTTCATCTTTTGTT
65 TAAATCCTTTCATCTTTTGTT
* * * * * *
1154269 GACTTGTCGGTTCATTCCCAGTCAACCTTTTGTATCTTTTGTTTACCTATTGACTTAGTCTTAGG
1 GACTTGTCAGTTCATTCCAAGTCAACCTTTT-TATCCTTTGTTTACATGTTGACTTAGTCTCAGG
* *
1154334 -CAACCCATTTCATCTTTTGTT
65 TAAATCC-TTTCATCTTTTGTT
1154355 GAC
1 GAC
1154358 CTAACTGCCT
Statistics
Matches: 148, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
83 2 0.01
84 49 0.33
85 53 0.36
86 44 0.30
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (85 bp):
GACTTGTCAGTTCATTCCAAGTCAACCTTTTTATCCTTTGTTTACATGTTGACTTAGTCTCAGGT
AAATCCTTTCATCTTTTGTT
Found at i:1155745 original size:11 final size:12
Alignment explanation
Indices: 1155714--1155743 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1155704 GCAAATAGGA
*
1155714 AAAAAAAGATAG
1 AAAAAAAGAGAG
1155726 AAAAAAAGAGAG
1 AAAAAAAGAGAG
1155738 AAAAAA
1 AAAAAA
1155744 GAAAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (12 bp):
AAAAAAAGAGAG
Found at i:1156415 original size:13 final size:13
Alignment explanation
Indices: 1156397--1156423 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1156387 ACATTATGCT
1156397 TTGTATCGATACA
1 TTGTATCGATACA
1156410 TTGTATCGATACA
1 TTGTATCGATACA
1156423 T
1 T
1156424 GGACAATTGT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1156518 original size:33 final size:33
Alignment explanation
Indices: 1156476--1156538 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1156466 CCACTGTTTA
*
1156476 TATCGATACATGGT-ACATGGTATCGATACAATG
1 TATCGATACATGATGA-ATGGTATCGATACAATG
*
1156509 TATCGATACATGATGAATTGTATCGATACA
1 TATCGATACATGATGAATGGTATCGATACA
1156539 TTGCTTGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (33 bp):
TATCGATACATGATGAATGGTATCGATACAATG
Found at i:1160027 original size:13 final size:13
Alignment explanation
Indices: 1160009--1160034 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1159999 TACAGCAAGT
1160009 ATGTATCGATACA
1 ATGTATCGATACA
1160022 ATGTATCGATACA
1 ATGTATCGATACA
1160035 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1163712 original size:13 final size:13
Alignment explanation
Indices: 1163694--1163718 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1163684 TTTTCCAGAT
1163694 TGTATCGATACAA
1 TGTATCGATACAA
1163707 TGTATCGATACA
1 TGTATCGATACA
1163719 TTGCTTCAGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1165742 original size:13 final size:13
Alignment explanation
Indices: 1165724--1165749 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1165714 TACAGCAAGT
1165724 ATGTATCGATACA
1 ATGTATCGATACA
1165737 ATGTATCGATACA
1 ATGTATCGATACA
1165750 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1169559 original size:13 final size:13
Alignment explanation
Indices: 1169541--1169567 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1169531 ACAACATGCC
1169541 TTGTATCGATACA
1 TTGTATCGATACA
1169554 TTGTATCGATACA
1 TTGTATCGATACA
1169567 T
1 T
1169568 GGGTTACTAT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1171497 original size:13 final size:13
Alignment explanation
Indices: 1171479--1171504 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1171469 TGATTAAGGG
1171479 GGAGAAATTTTTT
1 GGAGAAATTTTTT
1171492 GGAGAAATTTTTT
1 GGAGAAATTTTTT
1171505 TTAAATCTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (13 bp):
GGAGAAATTTTTT
Found at i:1172092 original size:13 final size:13
Alignment explanation
Indices: 1172074--1172100 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1172064 ACATTATGCT
1172074 TTGTATCGATACA
1 TTGTATCGATACA
1172087 TTGTATCGATACA
1 TTGTATCGATACA
1172100 T
1 T
1172101 GGACAATTGT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1172175 original size:20 final size:20
Alignment explanation
Indices: 1172150--1172243 Score: 138
Period size: 20 Copynumber: 4.7 Consensus size: 20
1172140 CTACCACTGT
*
1172150 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
1172170 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
*
1172190 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
1172210 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
1172230 TTGTATCGATACAT
1 TTGTATCGATACAT
1172244 TGCTTGTAAC
Statistics
Matches: 68, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.01
20 65 0.96
21 2 0.03
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:1172202 original size:40 final size:40
Alignment explanation
Indices: 1172150--1172243 Score: 188
Period size: 40 Copynumber: 2.4 Consensus size: 40
1172140 CTACCACTGT
1172150 TTGTATCGATACATGGTACATTGTATCGATACATGATGAA
1 TTGTATCGATACATGGTACATTGTATCGATACATGATGAA
1172190 TTGTATCGATACATGGTACATTGTATCGATACATGATGAA
1 TTGTATCGATACATGGTACATTGTATCGATACATGATGAA
1172230 TTGTATCGATACAT
1 TTGTATCGATACAT
1172244 TGCTTGTAAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (40 bp):
TTGTATCGATACATGGTACATTGTATCGATACATGATGAA
Found at i:1174372 original size:69 final size:69
Alignment explanation
Indices: 1174261--1174398 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
1174251 GTCCTAGGTT
1174261 GTCTCTTTTACACCAAAGGTGCACATATAGGTTAAACTCACTCTTAGCAATCCTTTTCCCCTAGG
1 GTCTCTTTTACACCAAAGGTGCACATATAGGTTAAACTCACTCTTAGCAATCCTTTTCCCCTAGG
1174326 ATCA
66 ATCA
1174330 GTCTCTTTTACACCAAAGGTGCACATATAGGTTAAACTCACTCTTAGCAATCCTTTTCCCCTAGG
1 GTCTCTTTTACACCAAAGGTGCACATATAGGTTAAACTCACTCTTAGCAATCCTTTTCCCCTAGG
1174395 ATCA
66 ATCA
1174399 CTGGGCACTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.32
Consensus pattern (69 bp):
GTCTCTTTTACACCAAAGGTGCACATATAGGTTAAACTCACTCTTAGCAATCCTTTTCCCCTAGG
ATCA
Found at i:1184205 original size:69 final size:69
Alignment explanation
Indices: 1184094--1184223 Score: 233
Period size: 69 Copynumber: 1.9 Consensus size: 69
1184084 ACTAATTATC
* * *
1184094 CTTAGGAATACTTGTGATTACATAGTATTTCTCTCTTAAATTGAACTTAAGAATATAGAAGGATC
1 CTTAGGAATACTTGTGATTACATAGCATTTCTCTCTCAAATTGAACCTAAGAATATAGAAGGATC
1184159 ATCT
66 ATCT
1184163 CTTAGGAATACTTGTGATTACATAGCATTTCTCTCTCAAATTGAACCTAAGAATATAGAAG
1 CTTAGGAATACTTGTGATTACATAGCATTTCTCTCTCAAATTGAACCTAAGAATATAGAAG
1184224 AGGCCATAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (69 bp):
CTTAGGAATACTTGTGATTACATAGCATTTCTCTCTCAAATTGAACCTAAGAATATAGAAGGATC
ATCT
Found at i:1185958 original size:20 final size:20
Alignment explanation
Indices: 1185933--1185971 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1185923 TGGATTTTTC
*
1185933 CAAAATGTATCGATACATTG
1 CAAAATGTATCAATACATTG
1185953 CAAAATGTATCAATACATT
1 CAAAATGTATCAATACATT
1185972 TGGATTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (20 bp):
CAAAATGTATCAATACATTG
Found at i:1188081 original size:95 final size:98
Alignment explanation
Indices: 1187881--1188062 Score: 280
Period size: 99 Copynumber: 1.9 Consensus size: 98
1187871 AGTGAGAATG
* *
1187881 TTTTAAGGGGGAGAAATAGAGAATATAAAGAAGTGTTATAGAAGGAGAAATTAGAGAAATTTGTA
1 TTTTAAAGGGCAGAAATAGAGAATATAAAGAAGTGTTATAGAA-GAGAAATTAGAGAAATTTGTA
*
1187946 TAAAATTATCTTATAACATAAAAAGGGAGAAACA
65 TAAAATTATCTTATAACACAAAAAGGGAGAAACA
* *
1187980 TTTTAAAGGGCAGAAATAGAGAATATAAAGAAGTGTTATA-AA-AG-GATTGGAGAAATTTGTAT
1 TTTTAAAGGGCAGAAATAGAGAATATAAAGAAGTGTTATAGAAGAGAAATTAGAGAAATTTGTAT
*
1188042 AAAATTGTCTTATAACACAAA
66 AAAATTATCTTATAACACAAA
1188063 TGGGGAGAGC
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
95 35 0.45
96 2 0.03
98 2 0.03
99 38 0.49
ACGTcount: A:0.48, C:0.04, G:0.21, T:0.27
Consensus pattern (98 bp):
TTTTAAAGGGCAGAAATAGAGAATATAAAGAAGTGTTATAGAAGAGAAATTAGAGAAATTTGTAT
AAAATTATCTTATAACACAAAAAGGGAGAAACA
Found at i:1189141 original size:20 final size:20
Alignment explanation
Indices: 1189115--1189169 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1189105 CTGCCAAATT
1189115 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAG
*
1189135 TATGTATCGATACAA-TGAG
1 CATGTATCGATACAATTGAG
* *
1189154 CATATATCGACACAAT
1 CATGTATCGATACAAT
1189170 GTATCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:1189840 original size:21 final size:21
Alignment explanation
Indices: 1189806--1189854 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1189796 GTAAATTTTC
* *
1189806 AATAAATCTGCCCCTTAATAA
1 AATAATTCTCCCCCTTAATAA
*
1189827 AATAATTCTCCCCCTTGATAA
1 AATAATTCTCCCCCTTAATAA
1189848 AATAATT
1 AATAATT
1189855 AAAGCTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (21 bp):
AATAATTCTCCCCCTTAATAA
Found at i:1195896 original size:33 final size:33
Alignment explanation
Indices: 1195831--1195897 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
1195821 AATTCCCAGA
**
1195831 TGTATCGATACAAAGATCAATGTATCGGTACAT
1 TGTATCGATACAAAGATCAATGTATCAATACAT
1195864 TGTATCGATACATTAA-AT-AATGTATCAATACAT
1 TGTATCGATACA--AAGATCAATGTATCAATACAT
1195897 T
1 T
1195898 TTCTTGGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 26 0.87
34 2 0.07
35 2 0.07
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAAAGATCAATGTATCAATACAT
Found at i:1196980 original size:101 final size:96
Alignment explanation
Indices: 1196727--1197423 Score: 555
Period size: 87 Copynumber: 7.3 Consensus size: 96
1196717 GACAATGTGT
* * * * * * **
1196727 TGATTCATGGCCAGCGACATTAGACTTAAAGA-AGAATGCCAATCTGCTGAGACAAGGCCAGCGA
1 TGATTCAAGGCCAACGATATTGGACTTAAAGATA-AGTGCCAATGTGCTGATTCAAGGCCAGCGA
* * * *
1196791 CATTGGGCTTAGGAATGTTAAAGATGCCAATATGC
65 CATTGGTCTTA--AA-GATGAAGGTGCCAATATGC
*
1196826 TGATTCAA-GCCAACGATATTGGACTCAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCG
1 TGATTCAAGGCCAACGATATTGGACTTAAAGAT-AA-GTGCCAATGTGCTGATTCAAGGCCAGCG
* *
1196890 ACACTGGTCTTAAAGATGGTTAAGGTGCCAATGTGC
64 ACATTGGTCTTAAAGAT-G--AAGGTGCCAATATGC
* * * * **
1196926 TGATTCAAGGCCAATGACATCGGCCTTAAAGATAAAGTTGCCAATGTGCTGATTCAAGGCCAATG
1 TGATTCAAGGCCAACGATATTGGACTTAAAGAT-AAG-TGCCAATGTGCTGATTCAAGGCCAGCG
* *
1196991 AGATTGGTCTTAAAGATGAAGGTGCGAATATGC
64 ACATTGGTCTTAAAGATGAAGGTGCCAATATGC
* * * * *
1197024 TGATTCAAAGCCAACGATATGGGGC-T-----T--GTGCCAATGTGCTGATTCAAGGCTAGCGAT
1 TGATTCAAGGCCAACGATATTGGACTTAAAGATAAGTGCCAATGTGCTGATTCAAGGCCAGCGAC
* * * *
1197081 AGTGGTCTTAGAGA-CAAGGTGCCAATATAC
66 ATTGGTCTTAAAGATGAAGGTGCCAATATGC
* ** * *
1197111 TGATTCAAGGCTAGTGATATTGGGC-T-----T--GTGCCAATGTGCTGATTCAAGGCCAGCAAC
1 TGATTCAAGGCCAACGATATTGGACTTAAAGATAAGTGCCAATGTGCTGATTCAAGGCCAGCGAC
*
1197168 ATTGGTCTTAAAGA-CAAGGTGCCAATATGC
66 ATTGGTCTTAAAGATGAAGGTGCCAATATGC
* * * * *
1197198 TGATTCAAGGCCAGCGATATTGGACTCAAGATGGTAAAAGTGCCAATATGCTGATTCAAGGCCAA
1 TGATTCAAGGCCAACGATATTGGACTTAA-A--G-ATAAGTGCCAATGTGCTGATTCAAGGCCAG
* * *
1197263 CGATATTGGACTT----A--AAGGTGCCAATGTGC
62 CGACATTGGTCTTAAAGATGAAGGTGCCAATATGC
* * * *
1197292 TGATTCAAGGCCAGCGACATTAGTCTTAAAGATGGTTAAGGTGCCAATGTGCTGATTCAAGGCCA
1 TGATTCAAGGCCAACGATATTGGACTTAAAGA----TAA-GTGCCAATGTGCTGATTCAAGGCCA
* *
1197357 ACGACATCGGTCTTAAAGATGAAGGTGCCAATATGC
61 GCGACATTGGTCTTAAAGATGAAGGTGCCAATATGC
*
1197393 TGATTCAAGGCCTACGATATTGGACTTAAAG
1 TGATTCAAGGCCAACGATATTGGACTTAAAG
1197424 GTGCCACAAA
Statistics
Matches: 489, Mismatches: 78, Indels: 60
0.78 0.12 0.10
Matches are distributed among these distances:
87 111 0.23
88 37 0.08
89 1 0.00
90 1 0.00
91 1 0.00
92 1 0.00
93 1 0.00
94 41 0.08
95 36 0.07
97 3 0.01
98 54 0.11
99 43 0.09
100 58 0.12
101 101 0.21
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (96 bp):
TGATTCAAGGCCAACGATATTGGACTTAAAGATAAGTGCCAATGTGCTGATTCAAGGCCAGCGAC
ATTGGTCTTAAAGATGAAGGTGCCAATATGC
Found at i:1197081 original size:39 final size:39
Alignment explanation
Indices: 1197012--1197160 Score: 118
Period size: 39 Copynumber: 3.6 Consensus size: 39
1197002 AAAGATGAAG
* * * *
1197012 GTGCGAATATGCTGATTCAAAGCCAACGATATGGGGCTT
1 GTGCCAATATGCTGATTCAAGGCTAGCGATATGGGGCTT
* **
1197051 GTGCCAATGTGCTGATTCAAGGCTAGCGATAGTGGTCTTAGAGACAAG
1 GTGCCAATATGCTGATTCAAGGCTAGCGATA-TGG-----G-G-C-TT
* * *
1197099 GTGCCAATATACTGATTCAAGGCTAGTGATATTGGGCTT
1 GTGCCAATATGCTGATTCAAGGCTAGCGATATGGGGCTT
*
1197138 GTGCCAATGTGCTGATTCAAGGC
1 GTGCCAATATGCTGATTCAAGGC
1197161 CAGCAACATT
Statistics
Matches: 86, Mismatches: 15, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
39 47 0.55
40 4 0.05
41 1 0.01
42 1 0.01
45 1 0.01
46 1 0.01
47 3 0.03
48 28 0.33
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (39 bp):
GTGCCAATATGCTGATTCAAGGCTAGCGATATGGGGCTT
Found at i:1197298 original size:43 final size:43
Alignment explanation
Indices: 1197232--1197429 Score: 162
Period size: 43 Copynumber: 4.3 Consensus size: 43
1197222 CTCAAGATGG
* *
1197232 TAAAAGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAACGACATTGGACT
* * * *
1197275 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGTCT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAACGACATTGGACT
* * *
1197318 TAAAGATGGTTAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATCGGTCT
1 T----A-----AAGGTGCCAATATGCTGATTCAAGGCCAACGACATTGGACT
* *
1197370 TAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCTACGATATTGGACT
1 T----A--AAGGTGCCAATATGCTGATTCAAGGCCAACGACATTGGACT
1197419 TAAAGGTGCCA
1 TAAAGGTGCCA
1197430 CAAAGTTGTG
Statistics
Matches: 131, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
43 47 0.36
45 1 0.01
47 1 0.01
49 38 0.29
52 44 0.34
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (43 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAACGACATTGGACT
Found at i:1197355 original size:52 final size:49
Alignment explanation
Indices: 1197138--1197409 Score: 227
Period size: 52 Copynumber: 5.6 Consensus size: 49
1197128 TATTGGGCTT
* * ** *
1197138 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGA-CAAG
1 GTGCCAATGTGCTGATTCAAGGCCAACGACATCAGTCTTAAAGATGAAG
* * * ** * * *
1197186 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-TCAAGATGGTAAAA
1 GTGCCAATGTGCTGATTCAAGGCCAACGACATCAGTCTTAAAGAT-G--AAG
* * ** *
1197237 GTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTT----A--AAG
1 GTGCCAATGTGCTGATTCAAGGCCAACGACATCAGTCTTAAAGATGAAG
* *
1197280 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGTCTTAAAGATGGTTAAG
1 GTGCCAATGTGCTGATTCAAGGCCAACGACATCAGTCTTAAAGAT-G--AAG
*
1197332 GTGCCAATGTGCTGATTCAAGGCCAACGACATCGGTCTTAAAGATGAAG
1 GTGCCAATGTGCTGATTCAAGGCCAACGACATCAGTCTTAAAGATGAAG
* *
1197381 GTGCCAATATGCTGATTCAAGGCCTACGA
1 GTGCCAATGTGCTGATTCAAGGCCAACGA
1197410 TATTGGACTT
Statistics
Matches: 191, Mismatches: 19, Indels: 27
0.81 0.08 0.11
Matches are distributed among these distances:
43 36 0.19
47 6 0.03
48 34 0.18
49 30 0.16
51 39 0.20
52 46 0.24
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.24
Consensus pattern (49 bp):
GTGCCAATGTGCTGATTCAAGGCCAACGACATCAGTCTTAAAGATGAAG
Found at i:1197355 original size:95 final size:94
Alignment explanation
Indices: 1197138--1197404 Score: 309
Period size: 95 Copynumber: 2.7 Consensus size: 94
1197128 TATTGGGCTT
* *
1197138 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
1 GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTT----A-AAGGTGCCAATATGCTGATT
* * *
1197203 CAAGGCCAGCGATATTGGACTCAAGATGGTAAAA
61 CAAGGCCAGCGACATTAGACTAAAGATGGTAAAA
* * * *
1197237 GTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGG
1 GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGGTGCCAATATGCTGATTCAAGG
* * *
1197302 CCAGCGACATTAGTCTTAAAGATGGTTAAG
66 CCAGCGACATTAGAC-TAAAGATGGTAAAA
*
1197332 GTGCCAATGTGCTGATTCAAGGCCAACGACATCGGTCTTAAAGATGAAGGTGCCAATATGCTGAT
1 GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTT----A--AAGGTGCCAATATGCTGAT
1197397 TCAAGGCC
60 TCAAGGCC
1197405 TACGATATTG
Statistics
Matches: 144, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
94 36 0.25
95 47 0.33
99 35 0.24
101 26 0.18
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.24
Consensus pattern (94 bp):
GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGGTGCCAATATGCTGATTCAAGG
CCAGCGACATTAGACTAAAGATGGTAAAA
Found at i:1197564 original size:33 final size:33
Alignment explanation
Indices: 1197420--1198224 Score: 510
Period size: 33 Copynumber: 25.3 Consensus size: 33
1197410 TATTGGACTT
** *
1197420 AAAGGTGCCACAAAGTTGTGGACTT-AGAGGAAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGG-AA
*
1197453 AAAGGGATGCCACGGAGGTGTAGG-CTTGAAAA-GAA
1 AAA-GG-TGCCACGGAGTTGT-GGACTT-AAAAGGAA
* *
1197488 AAAGGATGCCACGGAGTCGTGGACTTAAAAAG-A
1 AAAGG-TGCCACGGAGTTGTGGACTTAAAAGGAA
*
1197521 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
1197554 CAAGGTGCCACGGAGTTGAGAACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
1197587 AAAGATGCCACGGAGTTGTGGACTTCAAA-G--
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
1197617 ---GGTGCCACAGAGTTGTGGACTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
1197647 CAAGGTGCCACGGAGTTGTGCACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * * *
1197680 CAAGATGCCACCGAGTTGTGGACTTAAAAGAAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* ** *
1197713 AAAGATGCCATAGAGTTGTGGACTTCAAA-G--
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
1197743 ---GGTGCCACGGAGTTGTGGACGTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
1197773 AAAGGGTGCCACAGAGTTATGGACTTAAAAGGAA
1 AAA-GGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
1197807 AAAGAGTGCCACGAATTTGTGGACTTAAAAGGAA
1 AAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAA
1197841 AAAGG-GACCACGGAGTTGTGGACTTAAAA-G--
1 AAAGGTG-CCACGGAGTTGTGGACTTAAAAGGAA
*
1197871 ---GGTGCCACAGAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
1197901 AAAGAGTGCCATGGAGTTGTGGGCTT-----TAA
1 AAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAA
*
1197930 AAAGGTGCCACGGAGCTGTGGACTTAAAA-G--
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
1197960 ---GGTGCCACAGAGTTGTGGACTTTGAAAA-GAA
1 AAAGGTGCCACGGAGTTGTGGAC-TT-AAAAGGAA
* * **
1197991 AAAGGTGCCACGAAGTCGTGGACTTTGAA-G-A
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * * *
1198022 AAAGATGCCACTGAGTCGTGGACTTTGAAA--AA
1 AAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGAA
** * *
1198054 AAA--TGCCACTAAGTCGTGGACTT---TGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * * * * ** *
1198082 AGAGATGCCACTGAGTCGTGCACTTTGAAGAAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * ** ** *
1198115 AAAGATGCCACTGAGTCATGGACTTGGAAGAAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * * ** *
1198148 AAAGATGCCACTGAGTCGTGGACTTTGAAGAAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* ** ** *
1198181 AAAGATGCCATTGAGTTGTGGACTTTGAAGAAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
1198214 AAAGATGCCAC
1 AAAGGTGCCAC
1198225 TAAGTCGTCG
Statistics
Matches: 637, Mismatches: 84, Indels: 102
0.77 0.10 0.12
Matches are distributed among these distances:
27 85 0.13
28 28 0.04
29 13 0.02
30 35 0.05
31 21 0.03
32 37 0.06
33 279 0.44
34 115 0.18
35 19 0.03
36 3 0.00
37 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.30, T:0.20
Consensus pattern (33 bp):
AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
Found at i:1197642 original size:93 final size:92
Alignment explanation
Indices: 1197413--1197898 Score: 360
Period size: 93 Copynumber: 5.1 Consensus size: 92
1197403 CCTACGATAT
* * * *
1197413 TGGACTT-AAA-GGTGCCACAAAGTTGTGGACTT-AGAGGAAAAAAGGGATGCCACGGAGGTGTA
1 TGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGG-AACAA-GG-TGCCACGGAGTTG-A
* *
1197475 GGCTTGAAAA-GAAAAAGGATGCCACGGAGTCG
62 GACTT-AAAAGGAAAAA-GATGCCACGGAGTTG
1197507 TGGACTTAAAAAGAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTG
1 TGGACTT-AAAAG----GGTGCCACAGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTG
1197572 AGAACTTAAAAGGAAAAAGATGCCACGGAGTTG
61 AG-ACTTAAAAGGAAAAAGATGCCACGGAGTTG
* * *
1197605 TGGACTTCAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGAACAAGGTGCCACGGAGTTGTGCAC
1 TGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGAG-AC
* *
1197670 TTAAAAGGAACAAGATGCCACCGAGTTG
65 TTAAAAGGAAAAAGATGCCACGGAGTTG
* * *
1197698 TGGACTTAAAAGAAAAAAGATGCCATAGAGTTGTGGACTTCAAA-G-----GGTGCCACGGAGTT
1 TGGACTTAAAAG------GGTGCCACAGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTT
* * * * *
1197757 GTGGACGTAAAAGGAAAAAGGGTGCCACAGAGTTA
60 G-AGACTTAAAAGGAAAAA-GATGCCACGGAGTTG
* *
1197792 TGGACTTAAAAGGAAAAAGAGTGCCAC-GAATTTGTGGACTTAAAAGGAAAAAGG-GACCACGGA
1 TGGACTTAAAA-G-----G-GTGCCACAG-AGTTGTGGACTTAAAAGGAACAAGGTG-CCACGGA
* *
1197855 GTTGTGGACTTAAAAGG-----G-TGCCACAGAGTTG
57 GTTG-AGACTTAAAAGGAAAAAGATGCCACGGAGTTG
1197886 TGGACTTAAAAGG
1 TGGACTTAAAAGG
1197899 AAAAAGAGTG
Statistics
Matches: 336, Mismatches: 28, Indels: 62
0.79 0.07 0.15
Matches are distributed among these distances:
88 1 0.00
93 116 0.35
94 61 0.18
95 21 0.06
96 4 0.01
97 4 0.01
98 28 0.08
99 44 0.13
100 3 0.01
101 50 0.15
102 4 0.01
ACGTcount: A:0.37, C:0.14, G:0.31, T:0.19
Consensus pattern (92 bp):
TGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGAGACT
TAAAAGGAAAAAGATGCCACGGAGTTG
Found at i:1197665 original size:126 final size:126
Alignment explanation
Indices: 1197488--1197960 Score: 609
Period size: 126 Copynumber: 3.8 Consensus size: 126
1197478 TTGAAAAGAA
* * *
1197488 AAAGGATGCCACGGAGTCGTGGACTTAAAAAG-AAAAGGTGCCACAGAGTTGTGGACTTAAAAGG
1 AAAGGGTGCCACAGAGTTGTGGACTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAAAAGG
* *
1197552 AACAAGGTGCCACGGAGTTGAGAACTTAAAAGGAAAAAGATGCCACGGAGTTGTGGACTTC
66 AACAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGATGCCACGGAGTTGTGGACTTC
* * *
1197613 AAAGGGTGCCACAGAGTTGTGGACTTAAAAAGAACAAGGTGCCACGGAGTTGTGCACTTAAAAGG
1 AAAGGGTGCCACAGAGTTGTGGACTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAAAAGG
* * * **
1197678 AACAAGATGCCACCGAGTTGTGGACTTAAAAGAAAAAAGATGCCATAGAGTTGTGGACTTC
66 AACAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGATGCCACGGAGTTGTGGACTTC
* * * *
1197739 AAAGGGTGCCACGGAGTTGTGGACGTAAAAGGAAAAAGGGTGCCACAGAGTTATGGACTTAAAAG
1 AAAGGGTGCCACAGAGTTGTGGACTTAAAAAGAAAAA-GGTGCCACAGAGTTGTGGACTTAAAAG
* * * * *
1197804 GAAAAAGAGTGCCACGAATTTGTGGACTTAAAAGGAAAAAG-GGACCACGGAGTTGTGGACTTA
65 GAACAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGATG-CCACGGAGTTGTGGACTTC
* ** * *
1197867 AAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTT--TA-
1 AAAGGGTGCCACAGAGTTGTGGACTTAAAAAGAAAAAG-GTGCCACAGAGTTGTGGACTTAAAAG
*
1197929 -AA-AAGGTGCCACGGAGCTGTGGACTTAAAAGG
65 GAACAAGGTGCCACGGAGTTGTGGACTTAAAAGG
1197961 GTGCCACAGA
Statistics
Matches: 303, Mismatches: 40, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
122 24 0.08
123 3 0.01
124 2 0.01
125 29 0.10
126 117 0.39
127 32 0.11
128 96 0.32
ACGTcount: A:0.36, C:0.14, G:0.31, T:0.19
Consensus pattern (126 bp):
AAAGGGTGCCACAGAGTTGTGGACTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAAAAGG
AACAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGATGCCACGGAGTTGTGGACTTC
Found at i:1197782 original size:34 final size:34
Alignment explanation
Indices: 1197739--1198015 Score: 231
Period size: 34 Copynumber: 8.8 Consensus size: 34
1197729 TGTGGACTTC
*
1197739 AAAGGGTGCCACGGAGTTGTGGACGTAAAAGGAA
1 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
1197773 AAAGGGTGCCACAGAGTTATGGACTTAAAAGGAA
1 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
1197807 AAAGAGTGCCACGAATTTGTGGACTTAAAAGGAA
1 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
1197841 AAAGGG-ACCACGGAGTTGTGGACTT-------A
1 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
1197867 AAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAA
1 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * * *
1197901 AAAGAGTGCCATGGAGTTGTGGGCTT-----TAA
1 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
1197930 AAA-GGTGCCACGGAGCTGTGGACTT-------A
1 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
1197956 AAAGGGTGCCACAGAGTTGTGGACTTTGAAAA-GAA
1 AAAGGGTGCCACGGAGTTGTGGAC-TT-AAAAGGAA
* *
1197991 AAA-GGTGCCACGAAGTCGTGGACTT
1 AAAGGGTGCCACGGAGTTGTGGACTT
1198016 TGAAGAAAAG
Statistics
Matches: 198, Mismatches: 28, Indels: 35
0.76 0.11 0.13
Matches are distributed among these distances:
26 11 0.06
27 35 0.18
28 20 0.10
29 5 0.03
33 18 0.09
34 105 0.53
35 4 0.02
ACGTcount: A:0.35, C:0.13, G:0.32, T:0.19
Consensus pattern (34 bp):
AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAA
Found at i:1197937 original size:28 final size:28
Alignment explanation
Indices: 1197839--1198053 Score: 139
Period size: 27 Copynumber: 7.2 Consensus size: 28
1197829 ACTTAAAAGG
1197839 AAAAAGG-GACCACGGAGTTGTGGAC-TT
1 AAAAAGGTG-CCACGGAGTTGTGGACTTT
* * *
1197866 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGACTT-----T
* *
1197899 AAAAAGAGTGCCATGGAGTTGTGGGCTTT
1 AAAAAG-GTGCCACGGAGTTGTGGACTTT
*
1197928 AAAAAGGTGCCACGGAGCTGTGGAC-TT
1 AAAAAGGTGCCACGGAGTTGTGGACTTT
* *
1197955 AAAAGGGTGCCACAGAGTTGTGGACTTT
1 AAAAAGGTGCCACGGAGTTGTGGACTTT
* *
1197983 GAAAAGAAAAAGGTGCCACGAAGTCGTGGACTTT
1 ------AAAAAGGTGCCACGGAGTTGTGGACTTT
* * *
1198017 GAAGAAAAGATGCCACTGAGTCGTGGACTTT
1 --A-AAAAGGTGCCACGGAGTTGTGGACTTT
1198048 GAAAAA
1 -AAAAA
1198054 AAATGCCACT
Statistics
Matches: 148, Mismatches: 24, Indels: 30
0.73 0.12 0.15
Matches are distributed among these distances:
27 45 0.30
28 20 0.14
29 10 0.07
30 2 0.01
31 24 0.16
33 5 0.03
34 42 0.28
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (28 bp):
AAAAAGGTGCCACGGAGTTGTGGACTTT
Found at i:1197978 original size:89 final size:90
Alignment explanation
Indices: 1197772--1198015 Score: 325
Period size: 89 Copynumber: 2.7 Consensus size: 90
1197762 CGTAAAAGGA
* *
1197772 AAAAGGGTGCCACAGAGTTATGGACTTAAAAGGAAAAAGAGTGCCACGAATTTGTGGACTTAAAA
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGAAGTTGTGGACTT---A
*
1197837 GGAAAAAGGGACCACGGAGTTGTGGACTT
63 -GAAAAAGGGACCACGGAGCTGTGGACTT
* * * *
1197866 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTT-TAA
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGAAGTTGTGGACTTAGAA
1197930 AAAGGTG-CCACGGAGCTGTGGACTT
66 AAAGG-GACCACGGAGCTGTGGACTT
*
1197955 AAAAGGGTGCCACAGAGTTGTGGACTTTGAAAA-GAAAAAG-GTGCCACGAAGTCGTGGACTT
1 AAAAGGGTGCCACAGAGTTGTGGAC-TT-AAAAGGAAAAAGAGTGCCACGAAGTTGTGGACTT
1198016 TGAAGAAAAG
Statistics
Matches: 136, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
89 66 0.49
90 10 0.07
91 4 0.03
94 56 0.41
ACGTcount: A:0.35, C:0.14, G:0.32, T:0.20
Consensus pattern (90 bp):
AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGAAGTTGTGGACTTAGAA
AAAGGGACCACGGAGCTGTGGACTT
Found at i:1198238 original size:33 final size:33
Alignment explanation
Indices: 1197962--1198782 Score: 997
Period size: 33 Copynumber: 25.7 Consensus size: 33
1197952 CTTAAAAGGG
* * * *
1197962 TGCCACAGAGTTGTGGACTTTGAAAAGAAAAAGG
1 TGCCACTGAGTCGTGGACTTTGAAGA-AAAAAGA
1197996 TGCCAC-GAAGTCGTGGACTTTGAAG--AAAAGA
1 TGCCACTG-AGTCGTGGACTTTGAAGAAAAAAGA
1198027 TGCCACTGAGTCGTGGACTTTG-A-AAAAAA-A
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* *
1198057 TGCCACTAAGTCGTGGACTTTG--G-AAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
*
1198087 TGCCACTGAGTCGTGCACTTTGAAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* *
1198120 TGCCACTGAGTCATGGACTTGGAAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
1198153 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* *
1198186 TGCCATTGAGTTGTGGACTTTGAAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* *
1198219 TGCCACTAAGTCGTCGACTTTGAAG--AAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
*
1198250 TGCCACTAAGTCGTGGACTTTGAAG--AAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* * * *
1198281 TGCCATTGGGTTGTGGACTTTGGAAAGAGAAAAGA
1 TGCCACTGAGTCGTGGACTTT-G-AAGAAAAAAGA
1198316 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* *
1198349 TGACACTGAGTCGTGGACTTTG--G-AAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
*
1198379 TGCCACTGAGTCATGGACTTTGAAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* *
1198412 TGCCACTAAGTCGTGGAC-TT--AGAAAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
1198442 TGCCACTGAGTCGTGGACTTTGAAG-AAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* * *
1198474 TGCCACTAAGTCGTGGAC-TT--AGAAAAGATA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
*
1198504 TGCCATTGAGTCGTGGACTTTGAAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
*
1198537 TGCCACTGAGTCGTGGACTTTGAAG--AAAAGT
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* * *
1198568 TGCCATTGAGTTGTGGACTTTAGAAAAAGAAAAGA
1 TGCCACTGAGTCGTGGACTTT-GAAGAA-AAAAGA
*
1198603 TGCCACTGAGTCATGGACTTTGAAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
*
1198636 TGCCACTGAGTCGTGGACTTTG--G-AAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* *
1198666 TGCCATTGAGTCGTGGACTTTGAAGAAAAAATA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* * *
1198699 TGCCACTAAGTCATGGAC-TT--AGAAAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
*
1198729 TGCCACTGAGTTGTGGACTTTGAAG--AAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
*
1198760 TGCCACTAAGTCGTGGACTTTGA
1 TGCCACTGAGTCGTGGACTTTGA
1198783 GAAGAGAGAT
Statistics
Matches: 683, Mismatches: 71, Indels: 69
0.83 0.09 0.08
Matches are distributed among these distances:
29 6 0.01
30 167 0.24
31 142 0.21
32 35 0.05
33 259 0.38
34 27 0.04
35 47 0.07
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (33 bp):
TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
Found at i:1198611 original size:287 final size:286
Alignment explanation
Indices: 1198018--1198779 Score: 1201
Period size: 287 Copynumber: 2.7 Consensus size: 286
1198008 GTGGACTTTG
*
1198018 AAGAAAAGATGCCACTGAGTCGTGGACTTTG-A-AAAAAA-ATGCCACTAAGTCGTGGACTTTGG
1 AAGAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGG
* *
1198080 AAAGAGATGCCACTGAGTCGTGCACTTTGAAGAAAAAAGATGCCACTGAGTCATGGACTTGGAAG
66 AAAGAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTAAGTCATGGACTT---AG
* * * *
1198145 AAAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCATTGAGTTGTGGACTTTGAA
128 AAAAGAGATGCCACTGAGTCGTGGACTTTGAAG-AAAAAGATGCCACTAAGTCGTGGAC-TT-AA
1198210 GAAAAAAGATGCCACTAAGTCGTCGACTTTGAAGAAAAGATGCCACTAAGTCGTGGACTTTGAAG
190 GAAAAAAGATGCCACTAAGTCGTCGACTTTGAAGAAAAGATGCCACTAAGTCGTGGACTTTGAAG
* *
1198275 AAAAGATGCCATTGGGTTGTGGACTTTGGAAA
255 AAAAGATGCCATTGAGTTGTGGACTTTAGAAA
* *
1198307 GAGAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGACACTGAGTCGTGGACTTTGG
1 AAGAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGG
* *
1198372 AAAGAGATGCCACTGAGTCATGGACTTTGAAGAAAAAAGATGCCACTAAGTCGTGGACTTAGAAA
66 AAAGAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTAAGTCATGGACTTAGAAA
*
1198437 AGAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAGATGCCACTAAGTCGTGGACTT-AGAAAAG
131 AGAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAGATGCCACTAAGTCGTGGACTTAAGAAAAA
* * * * *
1198501 ATATGCCATTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAA
196 AGATGCCACTAAGTCGTCGACTTTGAAG--AAAAGATGCCACTAAGTCGTGGACTTTGAAGAAAA
*
1198566 GTTGCCATTGAGTTGTGGACTTTAGAAA
259 GATGCCATTGAGTTGTGGACTTTAGAAA
*
1198594 AAGAAAAGATGCCACTGAGTCATGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGG
1 AAGAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGG
* *
1198659 AAAGAGATGCCATTGAGTCGTGGACTTTGAAGAAAAAATATGCCACTAAGTCATGGACTTAGAAA
66 AAAGAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTAAGTCATGGACTTAGAAA
*
1198724 AGAGATGCCACTGAGTTGTGGACTTTGAAG-AAAAGATGCCACTAAGTCGTGGACTT
131 AGAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAGATGCCACTAAGTCGTGGACTT
1198780 TGAGAAGAGA
Statistics
Matches: 440, Mismatches: 28, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
285 30 0.07
286 26 0.06
287 213 0.48
288 22 0.05
289 64 0.15
290 1 0.00
291 6 0.01
292 78 0.18
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (286 bp):
AAGAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGG
AAAGAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTAAGTCATGGACTTAGAAA
AGAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAGATGCCACTAAGTCGTGGACTTAAGAAAAA
AGATGCCACTAAGTCGTCGACTTTGAAGAAAAGATGCCACTAAGTCGTGGACTTTGAAGAAAAGA
TGCCATTGAGTTGTGGACTTTAGAAA
Found at i:1198792 original size:63 final size:64
Alignment explanation
Indices: 1197962--1198782 Score: 971
Period size: 63 Copynumber: 12.8 Consensus size: 64
1197952 CTTAAAAGGG
* * *
1197962 TGCCACAGAGTTGTGGACTTTGAAAAGAAAAAGGTGCCAC-GAAGTCGTGGACTTTGAAG--AAA
1 TGCCACTGAGTCGTGGACTTTG--AAG-AAAAGATGCCACTG-AGTCGTGGACTTTGAAGAAAAA
1198024 AGA
62 AGA
* * *
1198027 TGCCACTGAGTCGTGGACTTTGAA-AAAAAATGCCACTAAGTCGTGGACTTTG--G-AAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* * *
1198087 TGCCACTGAGTCGTGCACTTTGAAGAAAAAAGATGCCACTGAGTCATGGACTTGGAAGAAAAAAG
1 TGCCACTGAGTCGTGGACTTTGAAG--AAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAG
1198152 A
64 A
* *
1198153 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCATTGAGTTGTGGACTTTGAAGAAAAAAG
1 TGCCACTGAGTCGTGGACTTTGAAG--AAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAG
1198218 A
64 A
* * *
1198219 TGCCACTAAGTCGTCGACTTTGAAGAAAAGATGCCACTAAGTCGTGGACTTTGAAG--AAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* * *
1198281 TGCCATTGGGTTGTGGACTTTGGAAAGAGAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAA
1 TGCCACTGAGTCGTGGACTTT-G--A-AGAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAA
1198346 AGA
62 AGA
* *
1198349 TGACACTGAGTCGTGGACTTTG--GAAAGAGATGCCACTGAGTCATGGACTTTGAAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAA-AGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* * *
1198412 TGCCACTAAGTCGTGGACTTAGAA-AAGAGATGCCACTGAGTCGTGGACTTTGAAG-AAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* * * * *
1198474 TGCCACTAAGTCGTGGACTTAGAA-AAGATATGCCATTGAGTCGTGGACTTTGAAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
* * * *
1198537 TGCCACTGAGTCGTGGACTTTGAAGAAAAGTTGCCATTGAGTTGTGGACTTTAGAAAAAGAAAAG
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTT-GAAGAA-AAAAG
1198602 A
64 A
* *
1198603 TGCCACTGAGTCATGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTG--G-AAAGAG
1 TGCCACTGAGTCGTGGACTTTGAAG--AAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAG
1198665 A
64 A
* * * * *
1198666 TGCCATTGAGTCGTGGACTTTGAAGAAAAAATATGCCACTAAGTCATGGAC-TT--AGAAAAGAG
1 TGCCACTGAGTCGTGGACTTTGAAG--AAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAG
1198728 A
64 A
* *
1198729 TGCCACTGAGTTGTGGACTTTGAAGAAAAGATGCCACTAAGTCGTGGACTTTGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGA
1198783 GAAGAGAGAT
Statistics
Matches: 666, Mismatches: 62, Indels: 57
0.85 0.08 0.07
Matches are distributed among these distances:
59 1 0.00
60 28 0.04
61 46 0.07
62 91 0.14
63 218 0.33
64 54 0.08
65 27 0.04
66 152 0.23
67 2 0.00
68 47 0.07
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (64 bp):
TGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
Found at i:1207084 original size:13 final size:13
Alignment explanation
Indices: 1207066--1207093 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1207056 ATACAAAGAT
1207066 CAATGTATCGATA
1 CAATGTATCGATA
1207079 CAATGTATCGATA
1 CAATGTATCGATA
1207092 CA
1 CA
1207094 TTTCCTTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1207999 original size:23 final size:23
Alignment explanation
Indices: 1207973--1208021 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
1207963 ACCAAGCTCG
*
1207973 AGGAGCTTGTTTTAAACTATAAA
1 AGGAGCTTGTTTTAAACCATAAA
1207996 AGGAGCTTGTTTTAAACCATAAA
1 AGGAGCTTGTTTTAAACCATAAA
1208019 AGG
1 AGG
1208022 CTTTTGAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (23 bp):
AGGAGCTTGTTTTAAACCATAAA
Found at i:1213551 original size:13 final size:13
Alignment explanation
Indices: 1213533--1213559 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1213523 ATATTATGCT
1213533 TTGTATCGATACA
1 TTGTATCGATACA
1213546 TTGTATCGATACA
1 TTGTATCGATACA
1213559 T
1 T
1213560 GGACAACTGT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1213577 original size:20 final size:20
Alignment explanation
Indices: 1213547--1213600 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1213537 ATCGATACAT
*
1213547 TGTATCGATACATGGACAAC
1 TGTATCAATACATGGACAAC
* *
1213567 TGTATTAATACATGGACAAT
1 TGTATCAATACATGGACAAC
1213587 TGTATCAATACATG
1 TGTATCAATACATG
1213601 AAATTGGCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (20 bp):
TGTATCAATACATGGACAAC
Found at i:1215318 original size:52 final size:52
Alignment explanation
Indices: 1215184--1215687 Score: 361
Period size: 52 Copynumber: 9.8 Consensus size: 52
1215174 ATGAGAAATG
** * **
1215184 TGCCAATATATTGATTTAAGGCCAGCGATATTGGGGTTAAAGAT-ACGAAGAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA-GAAGAA
* * * * ** * * *
1215236 TGTCAATGTGTTGATTCACGGCCAATGACATTAGACTTGAAGATGAGAAGAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAGAAGAA
* * * ** *
1215288 TGCCAATATGCTAATTCAAGGCTAGCGACATTGGGTTTAGGAATG-TTA-AAG-A
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA--AA-GATGAGAAGAA
** *
1215340 TGCCAATATATTGATTCAAGGCCAGTGATATTGGACTTAAAGATGATG--G--
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA-GAAGAA
* *
1215389 TGCCAATCTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAGAAGAA
* ** * * * *
1215441 TACCAATGCGCTGATTCAAGGCTAGCAATATTGGACTTAAAGATGATAA-AGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAGAAGA-A
* ** * *
1215493 TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTGAGAA-AAAAAAAG-G
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-A-AAGATGAGAAGAA
* * * * * * *
1215545 TGCCAATGTGCTGATTCAAGGCTACCAACATTGGACTTAAAGATGATAA-ATG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAGAAGA-A
* *
1215597 TGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTT-AAGA-AAGAAGAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAGAAGAA
* * * *
1215647 GGTGCTAATGTCCTGATTCAAGGCCAGCGATATTAGACTTA
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
1215688 GAAGGAGATG
Statistics
Matches: 355, Mismatches: 75, Indels: 43
0.75 0.16 0.09
Matches are distributed among these distances:
48 1 0.00
49 42 0.12
50 11 0.03
51 11 0.03
52 274 0.77
53 9 0.03
54 6 0.02
55 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (52 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAGAAGAA
Found at i:1215530 original size:104 final size:103
Alignment explanation
Indices: 1215173--1215687 Score: 409
Period size: 104 Copynumber: 5.0 Consensus size: 103
1215163 AGATGATAAG
* * ** * ** *
1215173 GATGAGAAATGTGCCAATATATTGATTTAAGGCCAGCGATATTGGGGTTAAAGATACGAAGAATG
1 GATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA-AAGAAGAATG
* * * * *** * * *
1215238 TCAATGTGTTGATTCACGGCCAATGACATTAGACTTGAA
65 CCAATGCGCTGATTCAAGGCCAGCAATATTGGACTTAAA
* * * * * * * * *
1215277 GATGA-GAAGAATGCCAATATGCTAATTCAAGGCTAGCGACATTGG-GTTTAGGAATGTTAA-AG
1 GATGATAAAG-GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAAG--AAGA-
**** **
1215339 ATGCCAATATATTGATTCAAGGCCAGTGATATTGGACTTAAA
62 ATGCCAATGCGCTGATTCAAGGCCAGCAATATTGGACTTAAA
* * * *
1215381 GATGAT---GGTGCCAATCTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGAATA
1 GATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA-AAGAAGAATG
*
1215443 CCAATGCGCTGATTCAAGGCTAGCAATATTGGACTTAAA
65 CCAATGCGCTGATTCAAGGCCAGCAATATTGGACTTAAA
* * * *
1215482 GATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTGAGAAAAAAAAAG-GT
1 GATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-A-AAGAAAGAAGAAT
* * * *
1215546 GCCAATGTGCTGATTCAAGGCTACCAACATTGGACTTAAA
64 GCCAATGCGCTGATTCAAGGCCAGCAATATTGGACTTAAA
* *
1215586 GATGATAAATGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTT-AAGAAAGAAGAAGGT
1 GATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAAGAAGAA--T
* * *
1215650 GCTAATGTC-CTGATTCAAGGCCAGCGATATTAGACTTA
64 GCCAATG-CGCTGATTCAAGGCCAGCAATATTGGACTTA
1215688 GAAGGAGATG
Statistics
Matches: 333, Mismatches: 61, Indels: 34
0.78 0.14 0.08
Matches are distributed among these distances:
101 81 0.24
102 9 0.03
103 10 0.03
104 225 0.68
105 5 0.02
106 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (103 bp):
GATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAAGAAGAATGC
CAATGCGCTGATTCAAGGCCAGCAATATTGGACTTAAA
Found at i:1215615 original size:156 final size:155
Alignment explanation
Indices: 1215169--1215690 Score: 480
Period size: 156 Copynumber: 3.4 Consensus size: 155
1215159 TTGAAGATGA
* * * * * ** * **
1215169 TAAGGATGAGAAATGTGCCAATATATTGATTTAAGGCCAGCGATATTGGGGTTA-AAGATACGAA
1 TAAGAATGATAAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTGGACTTAGAA-AAAAAAA
* * * * * *** * *
1215233 GAATGTCAATGTGTTGATTCACGGCCAATGACATTAGACTTGAAGATGAGAAGAATGCCAATATG
65 G-GTGCCAATCTGCTGATTCAAGGCCACCAACATTGGACTTAAAGATGAGAAGAATGCCAATATG
* * **
1215298 CTAATTCAAGGCTAGCGACATTGGGTT
129 CTGATTCAAGGCTAGCGATATTGGACT
* * * * * * ** *
1215325 TAGGAATGTTAAAGATGCCAATATATTGATTCAAGGCCAGTGATATTGGACTT--AAAGATGATG
1 TAAGAATGATAAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTGGACTTAGAAAAAAAAAG
* * * **
1215388 GTGCCAATCTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGAATACCAATGCGCT
66 GTGCCAATCTGCTGATTCAAGGCCACCAACATTGGACTTAAAGATGAGAAGAATGCCAATATGCT
*
1215453 GATTCAAGGCTAGCAATATTGGACT
131 GATTCAAGGCTAGCGATATTGGACT
* *
1215478 TAA-AGATGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTGAGAAAAAAAA
1 TAAGA-ATGATAAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTGGACTT-AGAAAAAAAA
* * * *
1215542 AGGTGCCAATGTGCTGATTCAAGGCTACCAACATTGGACTTAAAGATGATAA-ATGTGCCAATAT
64 AGGTGCCAATCTGCTGATTCAAGGCCACCAACATTGGACTTAAAGATGAGAAGA-ATGCCAATAT
* *
1215606 GCTGATTCAAGGCCAGTGATATTGGACT
128 GCTGATTCAAGGCTAGCGATATTGGACT
* * * * *
1215634 TAAGAAAGA-AGAAGGTGCTAATGTCCTGATTCAAGGCCAGCGATATTAGACTTAGAA
1 TAAGAATGATA-AAGGTGCCAATATACTGATTCAAGGCCAGCGATATTGGACTTAGAA
1215691 GGAGATGCCA
Statistics
Matches: 300, Mismatches: 59, Indels: 15
0.80 0.16 0.04
Matches are distributed among these distances:
152 1 0.00
153 117 0.39
154 5 0.02
155 8 0.03
156 168 0.56
157 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (155 bp):
TAAGAATGATAAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTGGACTTAGAAAAAAAAAG
GTGCCAATCTGCTGATTCAAGGCCACCAACATTGGACTTAAAGATGAGAAGAATGCCAATATGCT
GATTCAAGGCTAGCGATATTGGACT
Found at i:1215759 original size:31 final size:31
Alignment explanation
Indices: 1215696--1215816 Score: 172
Period size: 32 Copynumber: 3.8 Consensus size: 31
1215686 TAGAAGGAGA
*
1215696 TGCCACT-AGCTTGTGTAGGCTTTTGAAAGGGT
1 TGCCACTGA-CTTGTGTGGGC-TTTGAAAGGGT
*
1215728 TGCCACTGACTTGTGTGGGCTTTGAATGGGT
1 TGCCACTGACTTGTGTGGGCTTTGAAAGGGT
*
1215759 TGCCACTGACTTGTGTGGGCTTTAAAAAGGGT
1 TGCCACTGACTTGTGTGGGCTTT-GAAAGGGT
*
1215791 TGCCACTAACTTGTGTGGGCTTTGAA
1 TGCCACTGACTTGTGTGGGCTTTGAA
1215817 GAAGGTTTCT
Statistics
Matches: 81, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
31 35 0.43
32 45 0.56
33 1 0.01
ACGTcount: A:0.18, C:0.17, G:0.31, T:0.34
Consensus pattern (31 bp):
TGCCACTGACTTGTGTGGGCTTTGAAAGGGT
Found at i:1215795 original size:63 final size:63
Alignment explanation
Indices: 1215696--1215816 Score: 190
Period size: 63 Copynumber: 1.9 Consensus size: 63
1215686 TAGAAGGAGA
** *
1215696 TGCCACTAGCTTGTGTAGGCTTTTGAAAGGGTTGCCACTGACTTGTGTGGGCTTTGAATGGGT
1 TGCCACTAGCTTGTGTAGGCTTTAAAAAGGGTTGCCACTAACTTGTGTGGGCTTTGAATGGGT
*
1215759 TGCCACT-GACTTGTGTGGGCTTTAAAAAGGGTTGCCACTAACTTGTGTGGGCTTTGAA
1 TGCCACTAG-CTTGTGTAGGCTTTAAAAAGGGTTGCCACTAACTTGTGTGGGCTTTGAA
1215817 GAAGGTTTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
62 1 0.02
63 52 0.98
ACGTcount: A:0.18, C:0.17, G:0.31, T:0.34
Consensus pattern (63 bp):
TGCCACTAGCTTGTGTAGGCTTTAAAAAGGGTTGCCACTAACTTGTGTGGGCTTTGAATGGGT
Found at i:1216054 original size:28 final size:27
Alignment explanation
Indices: 1215993--1216055 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
1215983 TATATACAGT
* *
1215993 AAGTGCCACTGATTGTGGATTTCGAAA
1 AAGTGCCACTAATTGTGGACTTCGAAA
* *
1216020 AAATGCCACTAACTTGTGGACTTCGAAG
1 AAGTGCCACTAA-TTGTGGACTTCGAAA
*
1216048 AGGTGCCA
1 AAGTGCCA
1216056 TTGTCTAGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
27 10 0.34
28 19 0.66
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (27 bp):
AAGTGCCACTAATTGTGGACTTCGAAA
Found at i:1218170 original size:19 final size:20
Alignment explanation
Indices: 1218130--1218181 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
1218120 TACAAGCCAA
1218130 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA-TTTTTG
1218151 TGTATCGATACATA-TTTTG
1 TGTATCGATACATATTTTTG
1218170 TGTATCGATACA
1 TGTATCGATACA
1218182 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 17 0.55
21 14 0.45
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (20 bp):
TGTATCGATACATATTTTTG
Found at i:1220580 original size:13 final size:13
Alignment explanation
Indices: 1220562--1220599 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1220552 ATAATCCCCC
1220562 TGTATCGATACAG
1 TGTATCGATACAG
*
1220575 TGTATCGATACAT
1 TGTATCGATACAG
1220588 TGTATCGATACA
1 TGTATCGATACA
1220600 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1223060 original size:13 final size:13
Alignment explanation
Indices: 1223042--1223067 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1223032 TAATTTTTTG
1223042 TGTATCGATACAT
1 TGTATCGATACAT
1223055 TGTATCGATACAT
1 TGTATCGATACAT
1223068 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1225625 original size:13 final size:13
Alignment explanation
Indices: 1225607--1225644 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1225597 ATAATCCCCC
1225607 TGTATCGATACAG
1 TGTATCGATACAG
*
1225620 TGTATCGATACAT
1 TGTATCGATACAG
1225633 TGTATCGATACA
1 TGTATCGATACA
1225645 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1227746 original size:15 final size:15
Alignment explanation
Indices: 1227726--1227756 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1227716 ATTTCGTTTC
*
1227726 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1227741 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1227756 G
1 G
1227757 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1229589 original size:21 final size:21
Alignment explanation
Indices: 1229560--1229604 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1229550 AAGTTTTCAT
*
1229560 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1229580 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1229602 TTT
1 TTT
1229605 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1231826 original size:13 final size:13
Alignment explanation
Indices: 1231808--1231833 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1231798 TAATTTTTTG
1231808 TGTATCGATACAT
1 TGTATCGATACAT
1231821 TGTATCGATACAT
1 TGTATCGATACAT
1231834 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1232631 original size:15 final size:15
Alignment explanation
Indices: 1232611--1232641 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1232601 ATTTCGTTTG
*
1232611 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1232626 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1232641 G
1 G
1232642 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1234474 original size:21 final size:21
Alignment explanation
Indices: 1234445--1234489 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1234435 AAGTTTTTAT
*
1234445 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1234465 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1234487 TTT
1 TTT
1234490 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1236729 original size:13 final size:13
Alignment explanation
Indices: 1236711--1236736 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1236701 ATATTTTTTG
1236711 TGTATCGATACAT
1 TGTATCGATACAT
1236724 TGTATCGATACAT
1 TGTATCGATACAT
1236737 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1236747 original size:32 final size:33
Alignment explanation
Indices: 1236690--1236754 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
1236680 TACAAGCCAA
1236690 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
1236724 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
1236755 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:1236748 original size:19 final size:19
Alignment explanation
Indices: 1236690--1236754 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
1236680 TACAAGCCAA
1236690 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
1236711 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
1236724 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
1236743 TGTATCGATACA
1 TGTATCGATACA
1236755 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:1236811 original size:21 final size:21
Alignment explanation
Indices: 1236785--1236841 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
1236775 ATTTCAATGA
1236785 CATGTATCGATACATCTTTTT
1 CATGTATCGATACATCTTTTT
1236806 CATGTATCGATACATCTTTTT
1 CATGTATCGATACATCTTTTT
1236827 CATGTATCGATACAT
1 CATGTATCGATACAT
1236842 TGCAACATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (21 bp):
CATGTATCGATACATCTTTTT
Found at i:1237209 original size:14 final size:13
Alignment explanation
Indices: 1237190--1237264 Score: 84
Period size: 14 Copynumber: 5.8 Consensus size: 13
1237180 CCTTTTCTTG
1237190 TTTGTTGTTTTTTT
1 TTTGTT-TTTTTTT
*
1237204 TTTGTTTTTTTTG
1 TTTGTTTTTTTTT
1237217 TTTG--TTTTTTT
1 TTTGTTTTTTTTT
*
1237228 TGTGTTTGTTTTTT
1 TTTGTTT-TTTTTT
1237242 TTTGTTTTTTTGTT
1 TTTGTTTTTTT-TT
1237256 TTT-TTTTTT
1 TTTGTTTTTT
1237265 GCGAAGGACG
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
11 9 0.17
13 21 0.40
14 23 0.43
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (13 bp):
TTTGTTTTTTTTT
Found at i:1237213 original size:9 final size:9
Alignment explanation
Indices: 1237199--1237261 Score: 76
Period size: 9 Copynumber: 6.9 Consensus size: 9
1237189 GTTTGTTGTT
1237199 TTTTTTTTG
1 TTTTTTTTG
1237208 TTTTTTTTG
1 TTTTTTTTG
1237217 TTTGTTTTT-
1 TTT-TTTTTG
*
1237226 TTTGTGTTTG
1 TTT-TTTTTG
1237236 TTTTTTTT-
1 TTTTTTTTG
1237244 TGTTTTTTTG
1 T-TTTTTTTG
1237254 TTTTTTTT
1 TTTTTTTT
1237262 TTTGCGAAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
8 1 0.02
9 38 0.79
10 9 0.19
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:1237226 original size:24 final size:24
Alignment explanation
Indices: 1237190--1237265 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
1237180 CCTTTTCTTG
1237190 TTTG-TTGTTTTTTTTTTGTTTTT
1 TTTGTTTGTTTTTTTTTTGTTTTT
*
1237213 TTTGTTTGTTTTTTTTGTGTTTGTT
1 TTTGTTTGTTTTTTTTTTGTTT-TT
*
1237238 TTTTTTTGTTTTTTTGTTT-TTTTT
1 TTTGTTTGTTTTTTT-TTTGTTTTT
1237262 TTTG
1 TTTG
1237266 CGAAGGACGC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
23 4 0.09
24 21 0.46
25 19 0.41
26 2 0.04
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (24 bp):
TTTGTTTGTTTTTTTTTTGTTTTT
Found at i:1237259 original size:33 final size:36
Alignment explanation
Indices: 1237190--1237261 Score: 105
Period size: 33 Copynumber: 2.1 Consensus size: 36
1237180 CCTTTTCTTG
* *
1237190 TTTGTTGTTTTTTTTTTGTTTTTTTTGTTTGTTTTT
1 TTTGTTGTTTGTTTTTTGTTTGTTTTGTTTGTTTTT
1237226 TTTG-TGTTTGTTTTTT-TTTGTTTT-TTTGTTTTT
1 TTTGTTGTTTGTTTTTTGTTTGTTTTGTTTGTTTTT
1237259 TTT
1 TTT
1237262 TTTGCGAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 12 0.35
34 7 0.21
35 11 0.32
36 4 0.12
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (36 bp):
TTTGTTGTTTGTTTTTTGTTTGTTTTGTTTGTTTTT
Found at i:1237281 original size:1 final size:1
Alignment explanation
Indices: 1237197--1237264 Score: 64
Period size: 1 Copynumber: 68.0 Consensus size: 1
1237187 TTGTTTGTTG
* * * * * * * *
1237197 TTTTTTTTTTGTTTTTTTTGTTTGTTTTTTTTGTGTTTGTTTTTTTTTGTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1237262 TTT
1 TTT
1237265 GCGAAGGACG
Statistics
Matches: 51, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (1 bp):
T
Found at i:1256484 original size:97 final size:97
Alignment explanation
Indices: 1256284--1256501 Score: 255
Period size: 97 Copynumber: 2.2 Consensus size: 97
1256274 TATTTCTTCG
* *
1256284 AGGGGATACTCCAACCTCATTTTTAAACTTGTTAAGATTTAAGTCTTATCTTTGCTGAAATTGTC
1 AGGGGATACTCCAACCTCATTTTTAAACTTGTCAAGATTTAAATCTTATCTTTGCTGAAATTGTC
* * *
1256349 ATCATTGAGGATACTCTAACCCCATCCTTTCA
66 ATCATTGAGGACACTCCAACCCCATCCTCTCA
* *
1256381 AGGGGATACTCCAGCCTCATTTTTAAACTTGTCAAGATTTAAATTTTAT-TCTTGCCT-AAATTG
1 AGGGGATACTCCAACCTCATTTTTAAACTTGTCAAGATTTAAATCTTATCT-TTG-CTGAAATTG
* * * *
1256444 TCATC-TTGGTGGACACTCCAATCCTATTCCTCTGA
64 TCATCATT-GAGGACACTCCAACCCCA-TCCTCTCA
*
1256479 A-GGGATACTCTAACCCTCATTTT
1 AGGGGATACTCCAA-CCTCATTTT
1256502 CAACCAAAAA
Statistics
Matches: 103, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
96 3 0.03
97 82 0.80
98 18 0.17
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (97 bp):
AGGGGATACTCCAACCTCATTTTTAAACTTGTCAAGATTTAAATCTTATCTTTGCTGAAATTGTC
ATCATTGAGGACACTCCAACCCCATCCTCTCA
Found at i:1257523 original size:21 final size:22
Alignment explanation
Indices: 1257497--1257537 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1257487 AAACTAAATT
1257497 AATTAATTAT-TCTTAATTAAA
1 AATTAATTATATCTTAATTAAA
*
1257518 AATTAATTATATTTTAATTA
1 AATTAATTATATCTTAATTA
1257538 TATTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTAATTATATCTTAATTAAA
Found at i:1257534 original size:11 final size:11
Alignment explanation
Indices: 1257520--1257555 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
1257510 TAATTAAAAA
1257520 TTAATTATATT
1 TTAATTATATT
1257531 TTAATTATATT
1 TTAATTATATT
1257542 TT-ATTATTATT
1 TTAATTA-TATT
1257553 TTA
1 TTA
1257556 TCTTTCCACC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.17
11 19 0.83
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTAATTATATT
Found at i:1257782 original size:18 final size:16
Alignment explanation
Indices: 1257759--1257801 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
1257749 AAGCAACGAC
1257759 AAACAAACAGT-AAGCAA
1 AAACAAACA-TCAAGC-A
1257776 GAAACAAACATCAAGCA
1 -AAACAAACATCAAGCA
1257793 AAACAAACA
1 AAACAAACA
1257802 AAAAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.38
17 2 0.08
18 13 0.54
ACGTcount: A:0.65, C:0.21, G:0.09, T:0.05
Consensus pattern (16 bp):
AAACAAACATCAAGCA
Found at i:1257838 original size:21 final size:20
Alignment explanation
Indices: 1257814--1257892 Score: 81
Period size: 21 Copynumber: 4.0 Consensus size: 20
1257804 AAAAATAAGA
*
1257814 AATGAAATAGCAAAACAAAGC
1 AATGAAATAGCAAAGC-AAGC
*
1257835 AATGAAATAGC-AAGCAAGA
1 AATGAAATAGCAAAGCAAGC
* *
1257854 AATGAAACAGCAAAGTGAAGC
1 AATGAAATAGCAAAG-CAAGC
*
1257875 AAAGAAATAGC-AAGCAAG
1 AATGAAATAGCAAAGCAAG
1257893 AAAAAAAGCA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 16 0.33
20 9 0.19
21 23 0.48
ACGTcount: A:0.58, C:0.13, G:0.20, T:0.09
Consensus pattern (20 bp):
AATGAAATAGCAAAGCAAGC
Found at i:1257855 original size:40 final size:40
Alignment explanation
Indices: 1257810--1257895 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
1257800 CAAAAAAAAT
* *
1257810 AAGAAATGAAATAGCAAAACAAAGCAATGAAATAGCAAGC
1 AAGAAATGAAACAGCAAAACAAAGCAAAGAAATAGCAAGC
***
1257850 AAGAAATGAAACAGCAAAGTGAAGCAAAGAAATAGCAAGC
1 AAGAAATGAAACAGCAAAACAAAGCAAAGAAATAGCAAGC
1257890 AAGAAA
1 AAGAAA
1257896 AAAAGCAGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.60, C:0.12, G:0.20, T:0.08
Consensus pattern (40 bp):
AAGAAATGAAACAGCAAAACAAAGCAAAGAAATAGCAAGC
Found at i:1257940 original size:24 final size:24
Alignment explanation
Indices: 1257894--1257940 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1257884 GCAAGCAAGA
*
1257894 AAAAAAGCAGTAGTATAAAAAAAG
1 AAAAAAGCAGTAGAATAAAAAAAG
*
1257918 AAAATAGCAGTA-AATAAAGAAAA
1 AAAAAAGCAGTAGAATAAA-AAAA
1257941 TAGTAGTAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.68, C:0.04, G:0.15, T:0.13
Consensus pattern (24 bp):
AAAAAAGCAGTAGAATAAAAAAAG
Found at i:1257950 original size:25 final size:22
Alignment explanation
Indices: 1257902--1257981 Score: 75
Period size: 19 Copynumber: 4.0 Consensus size: 22
1257892 GAAAAAAAGC
*
1257902 AGTAGTA-TAAAAAAAGAAAAT
1 AGTAGTAGCAAAAAAAGAAAAT
* *
1257923 AGCAGT---AAATAAAGAAAAT
1 AGTAGTAGCAAAAAAAGAAAAT
1257942 AGTAGTAGCAAAAAAAGAAAAT
1 AGTAGTAGCAAAAAAAGAAAAT
*
1257964 -G--GTAGCAATAAAAGAAAA
1 AGTAGTAGCAAAAAAAGAAAA
1257982 AAACAGCACC
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
19 33 0.65
21 6 0.12
22 12 0.24
ACGTcount: A:0.64, C:0.04, G:0.17, T:0.15
Consensus pattern (22 bp):
AGTAGTAGCAAAAAAAGAAAAT
Found at i:1257974 original size:40 final size:41
Alignment explanation
Indices: 1257902--1257981 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
1257892 GAAAAAAAGC
*
1257902 AGTAGTATAAAAAAAGAAAATAGCAGTAAAT-AAAGAAAAT
1 AGTAGTACAAAAAAAGAAAATAGCAGTAAATAAAAGAAAAT
* * *
1257942 AGTAGTAGCAAAAAAAGAAAATGGTAG-CAATAAAAGAAAA
1 AGTAGTA-CAAAAAAAGAAAATAGCAGTAAATAAAAGAAAA
1257982 AAACAGCACC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 10 0.29
41 24 0.71
ACGTcount: A:0.64, C:0.04, G:0.17, T:0.15
Consensus pattern (41 bp):
AGTAGTACAAAAAAAGAAAATAGCAGTAAATAAAAGAAAAT
Found at i:1257976 original size:22 final size:21
Alignment explanation
Indices: 1257908--1257984 Score: 61
Period size: 22 Copynumber: 3.7 Consensus size: 21
1257898 AAGCAGTAGT
1257908 ATAAAAAAAGAAAA--TAGCA
1 ATAAAAAAAGAAAATGTAGCA
* * *
1257927 GTAAATAAAGAAAATAGTAGTA
1 ATAAAAAAAGAAAAT-GTAGCA
**
1257949 GCAAAAAAAGAAAATGGTAGCA
1 ATAAAAAAAGAAAAT-GTAGCA
1257971 ATAAAAGAAA-AAAA
1 ATAAAA-AAAGAAAA
1257985 CAGCACCAAC
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
19 12 0.27
22 30 0.67
23 3 0.07
ACGTcount: A:0.68, C:0.04, G:0.16, T:0.13
Consensus pattern (21 bp):
ATAAAAAAAGAAAATGTAGCA
Found at i:1260211 original size:150 final size:148
Alignment explanation
Indices: 1259829--1260427 Score: 542
Period size: 150 Copynumber: 4.0 Consensus size: 148
1259819 ATAATTTTTT
* * * ** * * * * *
1259829 AAACCAAGTCCTAAGTCATTACCGGGTTTGCTTTTATGCTAAAGGTGTACATTTAGGATAGGTTA
1 AAACCAAGTCCTAGGTCATCATCGGGTCCGCTTCTATGCCAAAGGTGCATATTTAGGATAGGTTC
** *
1259894 AT-CCTTTTACCT-TTTTAAGTCCTTTAGGGGTATTAGGTACTTTTATATTGAAGGTATCCTATA
66 ATACC-TTTA-CTATTTTAAGTCCTTTAGGGGTATCGGGTACTTTTATGTTGAAGGTATCCT-T-
*
1259957 AGGGCATTTTAGTATTTTTTCAA
127 AGGGCATTTTAGTA-ATTTTCAA
* * * * *
1259980 AAACCAAGTCCTAGGTCATCACCAGGTCCGCTTTTATGCCGAAGGTGTATATTTAGGATAGGTTC
1 AAACCAAGTCCTAGGTCATCATCGGGTCCGCTTCTATGCCAAAGGTGCATATTTAGGATAGGTTC
* * *
1260045 ATTCCTTTACCATTTTAAGTCCTTTAGGGGTATCGGGTACTTTTATGTTGAAGATATCGCTTAGG
66 ATACCTTTACTATTTTAAGTCCTTTAGGGGTATCGGGTACTTTTATGTTGAAGGTATC-CTTAGG
* *
1260110 AGTATTTTCA-TAATTTTCCA
130 -GCATTTT-AGTAATTTTCAA
* * ** **
1260130 AAACCAAGTCCTATGTTATCATCGGGTCAACTTCTATGCCAAAGGTGCATATTTAGGATAAATTC
1 AAACCAAGTCCTAGGTCATCATCGGGTCCGCTTCTATGCCAAAGGTGCATATTTAGGATAGGTTC
** * ** * * * *
1260195 ACCCCTTTACTGTTTTAAGTTATTTAAGGTTACTAGGATACTTTTATGTTGAAGGTATCCTTAGG
66 ATACCTTTACTATTTTAAGTCCTTTAGGGGTA-TCGGGTACTTTTATGTTGAAGGTATCCTTA-G
**
1260260 GGCATTTTAGTAATTTTTTA
129 GGCATTTTAGTAATTTTCAA
** *
1260280 AAACTGAGTCCTAGGTCATCATCGGATCCGCTTCTATGCCAAAGGTGCACT-TTTAGGATAGGTT
1 AAACCAAGTCCTAGGTCATCATCGGGTCCGCTTCTATGCCAAAGGTGCA-TATTTAGGATAGGTT
* * * * * * * *
1260344 CATACCTTTTCTTTTTTAAGT-CTTTCAGGGTTACCGGGATACTTTCATATCGAAAGTATACCCT
65 CATACCTTTACTATTTTAAGTCCTTT-AGGGGTATCGGG-TACTTTTATGTTGAAGGTAT--CCT
* *
1260408 AAGGGTATTTTAGTAATTTT
126 TAGGGCATTTTAGTAATTTT
1260428 TTATAACTAA
Statistics
Matches: 369, Mismatches: 66, Indels: 26
0.80 0.14 0.06
Matches are distributed among these distances:
149 6 0.02
150 198 0.54
151 156 0.42
152 9 0.02
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (148 bp):
AAACCAAGTCCTAGGTCATCATCGGGTCCGCTTCTATGCCAAAGGTGCATATTTAGGATAGGTTC
ATACCTTTACTATTTTAAGTCCTTTAGGGGTATCGGGTACTTTTATGTTGAAGGTATCCTTAGGG
CATTTTAGTAATTTTCAA
Found at i:1260450 original size:300 final size:300
Alignment explanation
Indices: 1259927--1260469 Score: 674
Period size: 300 Copynumber: 1.8 Consensus size: 300
1259917 TTAGGGGTAT
1259927 TAGGTACTTTTATATTGAAGGTATCCTATAAGGGCATTTTAGTATTTTTTCAAAAACCAAGTCCT
1 TAGGTACTTTTATATTGAAGGTATCCTATAAGGGCATTTTAGTATTTTTT-AAAAACCAAGTCCT
* * * *
1259992 AGGTCATCACCAGGTCCGCTTTTATGCCGAAGGTGTATATTTAGGATAGGTTCATTCCTTTACCA
65 AGGTCATCACCAGGTCCGCTTCTATGCCAAAGGTGCATATTTAGGATAGGTTCATACCTTTACCA
* * * * * *
1260057 TTTTAAGTCCTTTAGGGGTATCGGGTACTTTTATGTTGAAGATATCGCTTAGGAGTATTTTCATA
130 TTTTAAGTCCTTTAGGGGTACCGGGTACTTTCATATCGAAGATATCCCTAAGGAGTATTTTCATA
*
1260122 ATTTTCCAAAACCAAGTCCTATGTTATCA-TCGGGTCAACTTCTATGCCAAAGGTGCATATTTAG
195 ATTTTCCAAAACCAAGTCCTAGGTTATCACT-GGGTCAACTTCTATGCCAAAGGTGCATATTTAG
1260186 GATAAATTCACCCCTTTACTGTTTTAAGTTATTTAAGGTTAC
259 GATAAATTCACCCCTTTACTGTTTTAAGTTATTTAAGGTTAC
* * **
1260228 TAGGATACTTTTATGTTGAAGGTATCCT-TAGGGGCATTTTAGTAATTTTTT-AAAACTGAGTCC
1 TAGG-TACTTTTATATTGAAGGTATCCTATAAGGGCATTTTAGT-ATTTTTTAAAAACCAAGTCC
* *
1260291 TAGGTCATCATC-GGATCCGCTTCTATGCCAAAGGTGCACT-TTTAGGATAGGTTCATACCTTTT
64 TAGGTCATCACCAGG-TCCGCTTCTATGCCAAAGGTGCA-TATTTAGGATAGGTTCATACCTTTA
** *
1260354 CTTTTTTAAGT-CTTTCAGGGTTACCGGGATACTTTCATATCGAA-AGTATACCCTAAGG-GTAT
127 CCATTTTAAGTCCTTT-AGGGGTACCGGG-TACTTTCATATCGAAGA-TAT-CCCTAAGGAGTAT
** * * * * *
1260416 TTT-AGTAATTTTTTATAACTAAG-CTTAGGTTATCACTGGGTCTACTTTTATGCC
188 TTTCA-TAATTTTCCAAAACCAAGTCCTAGGTTATCACTGGGTCAACTTCTATGCC
1260470 GAGGGTGATC
Statistics
Matches: 205, Mismatches: 27, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
299 6 0.03
300 108 0.53
301 56 0.27
302 35 0.17
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (300 bp):
TAGGTACTTTTATATTGAAGGTATCCTATAAGGGCATTTTAGTATTTTTTAAAAACCAAGTCCTA
GGTCATCACCAGGTCCGCTTCTATGCCAAAGGTGCATATTTAGGATAGGTTCATACCTTTACCAT
TTTAAGTCCTTTAGGGGTACCGGGTACTTTCATATCGAAGATATCCCTAAGGAGTATTTTCATAA
TTTTCCAAAACCAAGTCCTAGGTTATCACTGGGTCAACTTCTATGCCAAAGGTGCATATTTAGGA
TAAATTCACCCCTTTACTGTTTTAAGTTATTTAAGGTTAC
Found at i:1261919 original size:23 final size:22
Alignment explanation
Indices: 1261888--1261936 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
1261878 CGTCCCTCCT
**
1261888 TTTTATGTATTTTTGTGTGTTTA
1 TTTTATGTAAATTTGTGTG-TTA
* *
1261911 TTTTGTGTAAATTTGTTTGTTA
1 TTTTATGTAAATTTGTGTGTTA
1261933 TTTT
1 TTTT
1261937 CTTCTTTTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.14, C:0.00, G:0.16, T:0.69
Consensus pattern (22 bp):
TTTTATGTAAATTTGTGTGTTA
Found at i:1272844 original size:151 final size:152
Alignment explanation
Indices: 1272514--1273193 Score: 559
Period size: 151 Copynumber: 4.5 Consensus size: 152
1272504 AAACAAATCA
* * * * * * *
1272514 AACCTATCCCTAGATGAT-CACCCTCAGCATAAAAGCAGACCCGATGATAACCTAAGACTTGGTT
1 AACCTAT-CCTAAAT-ATACACCTTCAGCATAGAAGTAGACCCGGTGATGACCTAGGACTTGGTT
* ** * * * * * *
1272578 TT-GAAAAAATTACTAAAATGCCCCTAGGATATACTTTCGACGTGAAAGTGT-T--TTA---GTA
64 TTAG-AAAAATTATTAAAATGCCCCTAGGGGATACCTTCGACATAAAAGTATCTCAATACCCCTA
* * * **
1272636 AAGGACTTAAAAAAGAAAAAGTATG
128 AAAGACTTAAAACAGTAAAAGGGTG
* * ** * * *
1272661 AACCTATCTTAAA-AGAACACCTTTGGCTTAGAAGTGGACCCCGTGATGACCTAGGACTTGGTTT
1 AACCTATCCTAAATA-TACACCTTCAGCATAGAAGTAGACCCGGTGATGACCTAGGACTTGGTTT
* * * * *
1272725 TA-AAAAATTATTAAAATGCCCCTAAGGGATACCTTCAATATTAAAGTATCTCAATAACCCTAAA
65 TAGAAAAATTATTAAAATGCCCCTAGGGGATACCTTCGACATAAAAGTATCTCAATACCCCTAAA
1272789 AGACTTAAAACAGTAAAAGGGTG
130 AGACTTAAAACAGTAAAAGGGTG
* * * * *
1272812 AACCTATCCTACATATACA-CTCTCGGCATAGAAGTGGACCTGGTGAT-AACTCAGGACTTGGTT
1 AACCTATCCTAAATATACACCT-TCAGCATAGAAGTAGACCCGGTGATGACCT-AGGACTTGGTT
* * * * *
1272875 TT-GGAAAATTATGAAAAGGCCCCTAGGGGATATCTTCGACATAAAAGTA-CTCGATACCCCTAA
64 TTAGAAAAATTATTAAAATGCCCCTAGGGGATACCTTCGACATAAAAGTATCTCAATACCCCTAA
*
1272938 AAGACTTAAAAC-GATAAAAGGATG
129 AAGACTTAAAACAG-TAAAAGGGTG
* * * * * * * *
1272962 AACCTATTCTAAATATACACCTTCAACATAGAAGCAAACTCGGTGATAACTTAGGACATGGTTTT
1 AACCTATCCTAAATATACACCTTCAGCATAGAAGTAGACCCGGTGATGACCTAGGACTTGGTTTT
* * ** * *
1273027 AGAAAAAATACTAAAATGCCTTTAGGGGATACCTTCGACGTAAAAGTATC-CAATACCCCTAAAG
66 AGAAAAATTATTAAAATGCCCCTAGGGGATACCTTCGACATAAAAGTATCTCAATACCCCTAAAA
*
1273091 GACTTAAAA-AGGAAAAGGGATG
131 GACTTAAAACAGTAAAAGGG-TG
* * * * * *
1273113 AACCTATCCTAAATGTACACCTTCAGCGTA-ATAGTAGACCCAGTAATGACCTAGGACTCGGTTC
1 AACCTATCCTAAATATACACCTTCAGCATAGA-AGTAGACCCGGTGATGACCTAGGACTTGGTTT
*
1273177 TAGAAAAATTATCAAAA
65 TAGAAAAATTATTAAAA
1273194 GGTAAAGGGA
Statistics
Matches: 420, Mismatches: 92, Indels: 38
0.76 0.17 0.07
Matches are distributed among these distances:
144 1 0.00
145 37 0.09
146 42 0.10
147 7 0.02
148 2 0.00
149 1 0.00
150 92 0.22
151 236 0.56
152 2 0.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (152 bp):
AACCTATCCTAAATATACACCTTCAGCATAGAAGTAGACCCGGTGATGACCTAGGACTTGGTTTT
AGAAAAATTATTAAAATGCCCCTAGGGGATACCTTCGACATAAAAGTATCTCAATACCCCTAAAA
GACTTAAAACAGTAAAAGGGTG
Found at i:1273271 original size:93 final size:93
Alignment explanation
Indices: 1273097--1273280 Score: 253
Period size: 93 Copynumber: 2.0 Consensus size: 93
1273087 AAAGGACTTA
* *
1273097 AAAAGGAAAAGGGATGAACCTATCCTAAATGTACACCTTCAGCGTAATAGTAGACCCAGTAATGA
1 AAAAGGAAAAGGGATGAACCTATCCTAAATGTACACCTTCAGCATAAAAGTAGACCCAGTAATGA
*
1273162 CCTAGGACTCGGTTCTAGAAAAATTATC
66 CCTAGGACTCGATTCTAGAAAAATTATC
* * * *
1273190 AAAAGGTAAAGGGATGAACCTATCCTAAATGTACAGCTTCCGCATAAAAGTAGACTC-GATAATG
1 AAAAGGAAAAGGGATGAACCTATCCTAAATGTACACCTTCAGCATAAAAGTAGACCCAG-TAATG
** * *
1273254 ATGTATGACTTGATTCTAGAAAAATTA
65 ACCTAGGACTCGATTCTAGAAAAATTA
1273281 CTAAAATGCC
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
92 1 0.01
93 78 0.99
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (93 bp):
AAAAGGAAAAGGGATGAACCTATCCTAAATGTACACCTTCAGCATAAAAGTAGACCCAGTAATGA
CCTAGGACTCGATTCTAGAAAAATTATC
Found at i:1275136 original size:22 final size:22
Alignment explanation
Indices: 1275111--1275174 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
1275101 ATTATTGTTT
* * *
1275111 TTTTCTTTTTTTGCTTTTGCCG
1 TTTTCTTCTTTTGCTATTGCCA
* * *
1275133 TTTTCTTGTTTTGCTATTACTA
1 TTTTCTTCTTTTGCTATTGCCA
*
1275155 TTTTCTTCTTTTGCTGTTGC
1 TTTTCTTCTTTTGCTATTGC
1275175 TGCTACTACT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.05, C:0.17, G:0.12, T:0.66
Consensus pattern (22 bp):
TTTTCTTCTTTTGCTATTGCCA
Found at i:1275217 original size:20 final size:19
Alignment explanation
Indices: 1275192--1275350 Score: 61
Period size: 20 Copynumber: 8.3 Consensus size: 19
1275182 ACTTTGTTTC
1275192 TTGCTTGCTGTTTTGTTGCT
1 TTGCTTGCTGTTTT-TTGCT
* *
1275212 TTGCTTTGCTATTTTTT-TT
1 TTGC-TTGCTGTTTTTTGCT
* *
1275231 CTTGCTTGTTGTTTCTTTGGT
1 -TTGCTTGCTGTTT-TTTGCT
1275252 TTGCTTCGCTGTTTCATTT-C-
1 TTGCTT-GCTGTTT--TTTGCT
*
1275272 TTGCTTGTTGTTTCATTT-C-
1 TTGCTTGCTGTTT--TTTGCT
1275291 TTG-TT--T-TTTTTTCGCT
1 TTGCTTGCTGTTTTTT-GCT
*
1275307 TTGCTTGATGTTTGTTT-C-
1 TTGCTTGCTGTTT-TTTGCT
* *
1275325 TTGCTTGTTGTTGTTTGCCT
1 TTGCTTGCTGTTTTTTG-CT
1275345 TTGCTT
1 TTGCTT
1275351 CCTTCTTCTC
Statistics
Matches: 111, Mismatches: 11, Indels: 34
0.71 0.07 0.22
Matches are distributed among these distances:
13 3 0.03
15 4 0.04
16 4 0.04
17 5 0.05
18 13 0.12
19 26 0.23
20 34 0.31
21 19 0.17
22 3 0.03
ACGTcount: A:0.03, C:0.15, G:0.19, T:0.64
Consensus pattern (19 bp):
TTGCTTGCTGTTTTTTGCT
Found at i:1275234 original size:40 final size:40
Alignment explanation
Indices: 1275188--1275285 Score: 126
Period size: 40 Copynumber: 2.5 Consensus size: 40
1275178 TACTACTTTG
* * **
1275188 TTTCTTGCTTGCTGTTT-TGTTGCTTTGCTTTGCTATTTTT
1 TTTCTTGCTTGTTGTTTCT-TTGCTTTGCTTCGCTATTTCA
* *
1275228 TTTCTTGCTTGTTGTTTCTTTGGTTTGCTTCGCTGTTTCA
1 TTTCTTGCTTGTTGTTTCTTTGCTTTGCTTCGCTATTTCA
1275268 TTTCTTGCTTGTTGTTTC
1 TTTCTTGCTTGTTGTTTC
1275286 ATTTCTTGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
40 50 0.98
41 1 0.02
ACGTcount: A:0.02, C:0.16, G:0.18, T:0.63
Consensus pattern (40 bp):
TTTCTTGCTTGTTGTTTCTTTGCTTTGCTTCGCTATTTCA
Found at i:1275330 original size:18 final size:17
Alignment explanation
Indices: 1275307--1275340 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1275297 TTTTTTCGCT
1275307 TTGCTTGATGTTTGTTTC
1 TTGCTTGATG-TTGTTTC
*
1275325 TTGCTTGTTGTTGTTT
1 TTGCTTGATGTTGTTT
1275341 GCCTTTGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.03, C:0.09, G:0.24, T:0.65
Consensus pattern (17 bp):
TTGCTTGATGTTGTTTC
Found at i:1275990 original size:24 final size:24
Alignment explanation
Indices: 1275963--1276009 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1275953 TTTTGTTCGG
1275963 GTCACAAAATCTAGAAAAATGAAA
1 GTCACAAAATCTAGAAAAATGAAA
1275987 GTCACAAAATCTAGAAAAATGAA
1 GTCACAAAATCTAGAAAAATGAA
1276010 GCAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.57, C:0.13, G:0.13, T:0.17
Consensus pattern (24 bp):
GTCACAAAATCTAGAAAAATGAAA
Found at i:1276544 original size:44 final size:43
Alignment explanation
Indices: 1276367--1277319 Score: 387
Period size: 44 Copynumber: 21.7 Consensus size: 43
1276357 CAAATCGTTA
* * * * *
1276367 GACCAAGGTGGCAACCAAATGTCAAACAAAAAGGAGTTAGATTT
1 GACCAGGGTGGTAACCATACGTCAAACAAAAAGGAG-AAGATTT
* ** * * ** * *
1276411 GACTATAGTGGTAACCACACTTCAAATC-AAAATTAAAAGAATCT
1 GACCAGGGTGGTAACCATACGTCAAA-CAAAAAGGAGAAG-ATTT
* * * *
1276455 GACTAGGGTGGTAACCGTACGTCAAGCCGAAATGAGGA-AAG-TTT
1 GACCAGGGTGGTAACCATACGTCAA-AC-AAA-AAGGAGAAGATTT
*
1276499 GACCAGGGTGGTAACCATACGTCAAACAAAAAGGAGGCAGATTT
1 GACCAGGGTGGTAACCATACGTCAAACAAAAAGGA-GAAGATTT
* * * * * * * * *
1276543 GACCAAGGTGGTTACCATATGTTAAATC-ATAATGAAAATAATCT
1 GACCAGGGTGGTAACCATACGTCAAA-CAAAAAGGAGAA-GATTT
* * * * *
1276587 GACCAAGGTGATAACCATACGTCAAACCAAAATGAGAAAAGTTT
1 GACCAGGGTGGTAACCATACGTCAAACAAAAAGGAGAAGA-TTT
* * ** *
1276631 GACCAGGGTGATAACAATACAACAAACAAAAATGA-AAGGGATTT
1 GACCAGGGTGGTAACCATACGTCAAACAAAAAGGAGAA--GATTT
* * * * *
1276675 GACCAGGGTGGTAA-CATACGCCAAATC-AGAATGAAAAGAATCT
1 GACCAGGGTGGTAACCATACGTCAAA-CAAAAAGGAGAAG-ATTT
* * * *
1276718 AACCAGGGTGGTACCCATACGTCAAACCAAAATAAGAAAAG-TTT
1 GACCAGGGTGGTAACCATACGTCAAA-CAAAA-AGGAGAAGATTT
* * * * * *
1276762 AACCAAGGTGGTAACCATGCATCAAACAGAATA-GAGAAAAGTTT
1 GACCAGGGTGGTAACCATACGTCAAACA-AAAAGGAGAAGA-TTT
** * * * *
1276806 GACTGGGGTGATAACCATACATCAAACAAAAATGAGAGGGATTT
1 GACCAGGGTGGTAACCATACGTCAAACAAAAAGGAGA-AGATTT
* * * * * *
1276850 GACCTGGGTGGTAA-CATACGCCAAATC-AGAATGAAAAGAATCT
1 GACCAGGGTGGTAACCATACGTCAAA-CAAAAAGGAGAAG-ATTT
* * * *
1276893 AACCAGGGTGGTACCCATACGTCAAACCAAAATAAGAAAAG-TTT
1 GACCAGGGTGGTAACCATACGTCAAA-CAAAA-AGGAGAAGATTT
* * * * * *
1276937 AACCAAGGTGGTAACCATGCATCAAACAGAATA-GAGAAAAGTTT
1 GACCAGGGTGGTAACCATACGTCAAACA-AAAAGGAGAAGA-TTT
** * * * *
1276981 GACTGGGGTGATAACCATACATCAAACAAAAATGAGAGGGATTT
1 GACCAGGGTGGTAACCATACGTCAAACAAAAAGGAGA-AGATTT
* * * * *
1277025 GACCAGGGTGGTAA-CATACGCCAAATC-AGAATGAAAAGAATCT
1 GACCAGGGTGGTAACCATACGTCAAA-CAAAAAGGAGAAG-ATTT
* * * * * *
1277068 AACCAGGGTGGTACCCATACGTCAGACCAAAATGAGAAAAGTTT
1 GACCAGGGTGGTAACCATACGTCAAACAAAAAGGAGAAGA-TTT
* *
1277112 GACCTGGTTGGTAACCATACGTCAAACAGAAAA-GA-AAGGGATTT
1 GACCAGGGTGGTAACCATACGTCAAACA-AAAAGGAGAA--GATTT
** * * * * *
1277156 GACCAGGGTGGTAACCATACGTCAAATTAGAATGAAAATAATCT
1 GACCAGGGTGGTAACCATACGTCAAACAAAAAGGAGAA-GATTT
* * * * * *
1277200 GACTAGGGTGGTAACTATGCATCAAATGAAAATGAGAGAAG-TTT
1 GACCAGGGTGGTAACCATACGTCAAA-CAAAAAG-GAGAAGATTT
* * * * **
1277244 GACCACGGTGGTAACCATATGTCAAATAGAAAGGA-AAGGGAAAT
1 GACCAGGGTGGTAACCATACGTCAAACAAAAAGGAGAA--GATTT
* * *
1277288 GACCAGGGTGATGACCATATGTCAAATCAAAA
1 GACCAGGGTGGTAACCATACGTCAAA-CAAAA
1277320 TTAAAAAAAT
Statistics
Matches: 685, Mismatches: 172, Indels: 103
0.71 0.18 0.11
Matches are distributed among these distances:
41 6 0.01
42 16 0.02
43 125 0.18
44 492 0.72
45 21 0.03
46 23 0.03
47 2 0.00
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (43 bp):
GACCAGGGTGGTAACCATACGTCAAACAAAAAGGAGAAGATTT
Found at i:1276608 original size:132 final size:131
Alignment explanation
Indices: 1276367--1276789 Score: 440
Period size: 132 Copynumber: 3.2 Consensus size: 131
1276357 CAAATCGTTA
* * ** * * * *
1276367 GACCAAGGTGGCAACCAAATGTCAAACAAAAAGGAGTTAGATTTGACTATA-GTGGTAACCACAC
1 GACCAAGGTGGTAACCATACATCAAACAAAAAGGAG-GAGATTTGACCA-AGGTGGTTACCATA-
* * * * * *
1276431 T-TCAAATCAAAATTAAAAGAATCTGACTAGGGTGGTAACCGTACGTCAAGCCGAAATGAGGAAA
63 TGTCAAATCAAAATGAAAAGAATCTGACCAGGGTGGTAACCATACGTCAAACCAAAATGAGAAAA
1276495 GTTT
128 GTTT
* *
1276499 GACCAGGGTGGTAACCATACGTCAAACAAAAAGGAGGCAGATTTGACCAAGGTGGTTACCATATG
1 GACCAAGGTGGTAACCATACATCAAACAAAAAGGAGG-AGATTTGACCAAGGTGGTTACCATATG
* * * * *
1276564 TTAAATCATAATGAAAATAATCTGACCAAGGTGATAACCATACGTCAAACCAAAATGAGAAAAGT
65 TCAAATCAAAATGAAAAGAATCTGACCAGGGTGGTAACCATACGTCAAACCAAAATGAGAAAAGT
1276629 TT
130 TT
* * * * * * * *
1276631 GACCAGGGTGATAACAATACAACAAACAAAAATGAAAGG-GATTTGACCAGGGTGG-TAACATAC
1 GACCAAGGTGGTAACCATACATCAAACAAAAA-G-GAGGAGATTTGACCAAGGTGGTTACCATAT
* * * * *
1276694 GCCAAATCAGAATGAAAAGAATCTAACCAGGGTGGTACCCATACGTCAAACCAAAATAAGAAAAG
64 GTCAAATCAAAATGAAAAGAATCTGACCAGGGTGGTAACCATACGTCAAACCAAAATGAGAAAAG
1276759 TTT
129 TTT
* *
1276762 AACCAAGGTGGTAACCATGCATCAAACA
1 GACCAAGGTGGTAACCATACATCAAACA
1276790 GAATAGAGAA
Statistics
Matches: 244, Mismatches: 42, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
131 89 0.36
132 151 0.62
133 1 0.00
134 3 0.01
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.19
Consensus pattern (131 bp):
GACCAAGGTGGTAACCATACATCAAACAAAAAGGAGGAGATTTGACCAAGGTGGTTACCATATGT
CAAATCAAAATGAAAAGAATCTGACCAGGGTGGTAACCATACGTCAAACCAAAATGAGAAAAGTT
T
Found at i:1276868 original size:131 final size:131
Alignment explanation
Indices: 1276723--1276964 Score: 283
Period size: 131 Copynumber: 1.8 Consensus size: 131
1276713 AATCTAACCA
* * * *
1276723 GGGTGGTACCCATACGTCAAACCAAAATAAGAAAAG-TTTAACCAAGGTGGTAACCATGCATCAA
1 GGGTGGTACACATACGCCAAACCAAAAT--GAAAAGATCTAACCAAGGTGGTAACCATACATCAA
* * ***
1276787 A-CAGAATAGAGAAAAGTTTGACTGGGGTGATAACCATACATCAAACAAAAATGAGAGGGATTTG
64 ACCAAAATA-AGAAAAGTTTAACCAAGGTGATAACCATACATCAAACAAAAATGAGAGGGATTTG
1276851 ACCT
128 ACCT
* * * * *
1276855 GGGTGGTA-ACATACGCCAAATCAGAATGAAAAGAATCTAACCAGGGTGGTACCCATACGTCAAA
1 GGGTGGTACACATACGCCAAACCAAAATGAAAAG-ATCTAACCAAGGTGGTAACCATACATCAAA
* *
1276919 CCAAAATAAGAAAAGTTTAACCAAGGTGGTAACCATGCATCAAACA
65 CCAAAATAAGAAAAGTTTAACCAAGGTGATAACCATACATCAAACA
1276965 GAATAGAGAA
Statistics
Matches: 91, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
129 6 0.07
131 71 0.78
132 14 0.15
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (131 bp):
GGGTGGTACACATACGCCAAACCAAAATGAAAAGATCTAACCAAGGTGGTAACCATACATCAAAC
CAAAATAAGAAAAGTTTAACCAAGGTGATAACCATACATCAAACAAAAATGAGAGGGATTTGACC
T
Found at i:1276982 original size:131 final size:129
Alignment explanation
Indices: 1276812--1277379 Score: 434
Period size: 132 Copynumber: 4.3 Consensus size: 129
1276802 GTTTGACTGG
* ** *
1276812 GGTGATAACCATACATCA-AACAAAAATGAG-AGGGATTTGACCTGGGTGGTAA-CATACGCCAA
1 GGTGGTAACCATACATCAGAAC-AAAATGAGAAAAG-TTTGACCTGGGTGGTAACCATACGTCAA
* * * * *
1276874 ATCAGAATGAAAAGAATCTAACCAGGGTGGTACCCATACGTCAAACCAAAATAAGAAAAG-TTTA
64 A-CAGAATGAAAGGGATTTGACCAGGGTGGTA-CCATACGTCAAACCAAAAT--GAAAAGATCTA
1276938 ACCAA
125 ACCAA
* * * *
1276943 GGTGGTAACCATGCATCA-AACAGAATAGAGAAAAGTTTGA-CTGGGGTGATAACCATACATCAA
1 GGTGGTAACCATACATCAGAACAAAAT-GAGAAAAGTTTGACCT-GGGTGGTAACCATACGTCAA
* * * * * *
1277006 ACAAAAATGAGAGGGATTTGACCAGGGTGGTAACATACGCCAAATCAGAATGAAAAGAATCTAAC
64 AC-AGAATGAAAGGGATTTGACCAGGGTGGTACCATACGTCAAACCAAAATGAAAAG-ATCTAAC
*
1277071 CAG
127 CAA
* * * *
1277074 GGTGGTACCCATACGTCAGACCAAAATGAGAAAAGTTTGACCTGGTTGGTAACCATACGTCAAAC
1 GGTGGTAACCATACATCAGAACAAAATGAGAAAAGTTTGACCTGGGTGGTAACCATACGTCAAAC
* ** * * * *
1277139 AGAAAAGAAAGGGATTTGACCAGGGTGGTAACCATACGTCAAATTAGAATGAAAATAATCTGACT
66 AG-AATGAAAGGGATTTGACCAGGGTGGT-ACCATACGTCAAACCAAAATGAAAA-GATCTAACC
*
1277204 AG
128 AA
* * * * ** *
1277206 GGTGGTAACTATGCATCA-AATGAAAATGAGAGAAGTTTGACCACGGTGGTAACCATATGTCAAA
1 GGTGGTAACCATACATCAGAA-CAAAATGAGAAAAGTTTGACCTGGGTGGTAACCATACGTCAAA
* * ** * * * * *
1277270 TAGAAAGGAAAGGGAAATGACCAGGGTGATGACCATATGTCAAATCAAAATTAAAAAAATCTAA-
65 CAG-AATGAAAGGGATTTGACCAGGGTGGT-ACCATACGTCAAACCAAAA-TGAAAAGATCTAAC
*
1277334 CACG
127 CA-A
** *
1277338 GGTGGTAACCATATGTCA-AACCAAAATAAGAAAAGTTTGACC
1 GGTGGTAACCATACATCAGAA-CAAAATGAGAAAAGTTTGACC
1277380 AAGTGAAGAC
Statistics
Matches: 354, Mismatches: 68, Indels: 29
0.78 0.15 0.06
Matches are distributed among these distances:
129 6 0.02
130 7 0.02
131 131 0.37
132 205 0.58
133 5 0.01
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (129 bp):
GGTGGTAACCATACATCAGAACAAAATGAGAAAAGTTTGACCTGGGTGGTAACCATACGTCAAAC
AGAATGAAAGGGATTTGACCAGGGTGGTACCATACGTCAAACCAAAATGAAAAGATCTAACCAA
Found at i:1277214 original size:175 final size:175
Alignment explanation
Indices: 1276588--1277181 Score: 935
Period size: 175 Copynumber: 3.4 Consensus size: 175
1276578 AAATAATCTG
* * * * ** *
1276588 ACCAAGGTGATAACCATACGTCAAACCAAAAT-GAGAAAAGTTTGACCAGGGTGATAACAATACA
1 ACCAAGGTGGTAACCATGCATCAAA-CAGAATAGAGAAAAGTTTGACTGGGGTGATAACCATACA
* *
1276652 ACAAACAAAAATGAAAGGGATTTGACCAGGGTGGTAACATACGCCAAATCAGAATGAAAAGAATC
65 TCAAACAAAAATGAGAGGGATTTGACCAGGGTGGTAACATACGCCAAATCAGAATGAAAAGAATC
1276717 TAACCAGGGTGGTACCCATACGTCAAACCAAAATAAGAAAAGTTTA
130 TAACCAGGGTGGTACCCATACGTCAAACCAAAATAAGAAAAGTTTA
1276763 ACCAAGGTGGTAACCATGCATCAAACAGAATAGAGAAAAGTTTGACTGGGGTGATAACCATACAT
1 ACCAAGGTGGTAACCATGCATCAAACAGAATAGAGAAAAGTTTGACTGGGGTGATAACCATACAT
*
1276828 CAAACAAAAATGAGAGGGATTTGACCTGGGTGGTAACATACGCCAAATCAGAATGAAAAGAATCT
66 CAAACAAAAATGAGAGGGATTTGACCAGGGTGGTAACATACGCCAAATCAGAATGAAAAGAATCT
1276893 AACCAGGGTGGTACCCATACGTCAAACCAAAATAAGAAAAGTTTA
131 AACCAGGGTGGTACCCATACGTCAAACCAAAATAAGAAAAGTTTA
1276938 ACCAAGGTGGTAACCATGCATCAAACAGAATAGAGAAAAGTTTGACTGGGGTGATAACCATACAT
1 ACCAAGGTGGTAACCATGCATCAAACAGAATAGAGAAAAGTTTGACTGGGGTGATAACCATACAT
1277003 CAAACAAAAATGAGAGGGATTTGACCAGGGTGGTAACATACGCCAAATCAGAATGAAAAGAATCT
66 CAAACAAAAATGAGAGGGATTTGACCAGGGTGGTAACATACGCCAAATCAGAATGAAAAGAATCT
* * *
1277068 AACCAGGGTGGTACCCATACGTCAGACCAAAATGAGAAAAGTTTG
131 AACCAGGGTGGTACCCATACGTCAAACCAAAATAAGAAAAGTTTA
* * * * ** *
1277113 ACC-TGGTTGGTAACCATACGTCAAACAGAA-A-AGAAAGGGATTTGACCAGGGTGGTAACCATA
1 ACCAAGG-TGGTAACCATGCATCAAACAGAATAGAGAAA-AG-TTTGACTGGGGTGATAACCATA
*
1277175 CGTCAAA
63 CATCAAA
1277182 TTAGAATGAA
Statistics
Matches: 393, Mismatches: 22, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
173 5 0.01
174 9 0.02
175 379 0.96
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (175 bp):
ACCAAGGTGGTAACCATGCATCAAACAGAATAGAGAAAAGTTTGACTGGGGTGATAACCATACAT
CAAACAAAAATGAGAGGGATTTGACCAGGGTGGTAACATACGCCAAATCAGAATGAAAAGAATCT
AACCAGGGTGGTACCCATACGTCAAACCAAAATAAGAAAAGTTTA
Found at i:1277357 original size:132 final size:132
Alignment explanation
Indices: 1276894--1277380 Score: 438
Period size: 132 Copynumber: 3.7 Consensus size: 132
1276884 AAAGAATCTA
* * * * * **
1276894 ACCAGGGTGGTACCCATACGTCAAACCAAAAT-AAGAAAAGTTTAAC-CAAGGTGGTAACCATGC
1 ACCAGGGTGGTA-CCATACGTCAAATCAGAATGAA-AAAAATCTAACAC-GGGTGGTAACCATAT
* * ** * * * *
1276957 ATCAAA-CAGAATAGAGAAAAGTTTGA-CTGGGGTGATAACCATACATCAAACA-AAAATGAGAG
63 GTCAAACCAAAAT-GAGAAAAGTTTGACCACGGTTGGTAACCATACGTCAAACAGAAAA-GAAAG
**
1277019 GGATTTG
126 GGAAATG
* * * * *
1277026 ACCAGGGTGGTAACATACGCCAAATCAGAATGAAAAGAATCTAAC-CAGGGTGGTACCCATACGT
1 ACCAGGGTGGTACCATACGTCAAATCAGAATGAAAAAAATCTAACAC-GGGTGGTAACCATATGT
* * *
1277090 CAGACCAAAATGAGAAAAGTTTGACC-TGGTTGGTAACCATACGTCAAACAGAAAAGAAAGGGAT
65 CAAACCAAAATGAGAAAAGTTTGACCACGGTTGGTAACCATACGTCAAACAGAAAAGAAAGGGAA
*
1277154 TTG
130 ATG
* * *
1277157 ACCAGGGTGGTAACCATACGTCAAATTAGAATGAAAATAATCTGACTA-GGGTGGTAA-C-TATG
1 ACCAGGGTGGT-ACCATACGTCAAATCAGAATGAAAAAAATCTAAC-ACGGGTGGTAACCATATG
** * * * *
1277219 CATCAAATGAAAATGAGAGAAGTTTGACCACGG-TGGTAACCATATGTCAAATAGAAAGGAAAGG
64 --TCAAACCAAAATGAGAAAAGTTTGACCACGGTTGGTAACCATACGTCAAACAGAAAAGAAAGG
1277283 GAAATG
127 GAAATG
* * * *
1277289 ACCAGGGTGATGACCATATGTCAAATCAAAATTAAAAAAATCTAACACGGGTGGTAACCATATGT
1 ACCAGGGTGGT-ACCATACGTCAAATCAGAATGAAAAAAATCTAACACGGGTGGTAACCATATGT
*
1277354 CAAACCAAAATAAGAAAAGTTTGACCA
65 CAAACCAAAATGAGAAAAGTTTGACCA
1277381 AGTGAAGACA
Statistics
Matches: 295, Mismatches: 47, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
130 3 0.01
131 98 0.33
132 187 0.63
133 3 0.01
134 4 0.01
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (132 bp):
ACCAGGGTGGTACCATACGTCAAATCAGAATGAAAAAAATCTAACACGGGTGGTAACCATATGTC
AAACCAAAATGAGAAAAGTTTGACCACGGTTGGTAACCATACGTCAAACAGAAAAGAAAGGGAAA
TG
Found at i:1277673 original size:5 final size:5
Alignment explanation
Indices: 1277663--1277694 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
1277653 AATATATATA
1277663 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
1277695 GAAAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1278209 original size:28 final size:28
Alignment explanation
Indices: 1278155--1278232 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
1278145 CAAGTAACAA
*
1278155 CAGCTGCAATAAGGAG-AGAAACTGATG
1 CAGCTACAATAAGGAGAAGAAACTGATG
* *
1278182 CAGCTATAATGAGGAGAAGAAACTGATG
1 CAGCTACAATAAGGAGAAGAAACTGATG
* *
1278210 CTGCTACAATAAAGAGAAGAAAC
1 CAGCTACAATAAGGAGAAGAAAC
1278233 CATAGCAATG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 13 0.30
28 30 0.70
ACGTcount: A:0.45, C:0.14, G:0.26, T:0.15
Consensus pattern (28 bp):
CAGCTACAATAAGGAGAAGAAACTGATG
Found at i:1280539 original size:98 final size:99
Alignment explanation
Indices: 1280367--1280560 Score: 309
Period size: 98 Copynumber: 2.0 Consensus size: 99
1280357 CCGTCAATGG
* * * *
1280367 TAGATCCTAAGAACATTTCACCAATTTTTATGAAACCGAATCTTAGGAAAACACCGGGTCTGCTT
1 TAGATCCTAAAAACATCTCACCAATTCTTATGAAACCGAATCCTAGGAAAACACCGGGTCTGCTT
*
1280432 TCATACCGAGGGT-GGTATTAGGATAGGTTCATC
66 TCATACCGAGCGTGGGTATTAGGATAGGTTCATC
* *
1280465 TAGATCCTAAAAACATCTCACCAATTCTTATGAAACCGAATCCTAGGAAAACACCGGGTTTGTTT
1 TAGATCCTAAAAACATCTCACCAATTCTTATGAAACCGAATCCTAGGAAAACACCGGGTCTGCTT
*
1280530 TCATGCCGAGCGTGGGTATTAGGATAGGTTC
66 TCATACCGAGCGTGGGTATTAGGATAGGTTC
1280561 GTCTTTTCTT
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
98 70 0.80
99 17 0.20
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (99 bp):
TAGATCCTAAAAACATCTCACCAATTCTTATGAAACCGAATCCTAGGAAAACACCGGGTCTGCTT
TCATACCGAGCGTGGGTATTAGGATAGGTTCATC
Found at i:1283802 original size:6 final size:6
Alignment explanation
Indices: 1283784--1283835 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
1283774 TCCTCTAAAT
* *
1283784 AAGAAA AA-CAA AAGAAA AAGAAA AAG--A AAGAGA AAGAAA AA-AAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
1283828 AAGAAA AA
1 AAGAAA AA
1283836 AGTATGAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 4 0.10
5 9 0.23
6 26 0.67
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:1283814 original size:27 final size:27
Alignment explanation
Indices: 1283784--1283835 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1283774 TCCTCTAAAT
*
1283784 AAGAAAAACAAAAGAAAAAGAAAAAGA
1 AAGAAAAACAAAAAAAAAAGAAAAAGA
* *
1283811 AAGAGAAAGAAAAAAAAAAGAAAAA
1 AAGAAAAACAAAAAAAAAAGAAAAA
1283836 AGTATGAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (27 bp):
AAGAAAAACAAAAAAAAAAGAAAAAGA
Found at i:1283836 original size:11 final size:11
Alignment explanation
Indices: 1283784--1283836 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
1283774 TCCTCTAAAT
*
1283784 AAGAAAAACAA
1 AAGAAAAAAAA
1283795 AAGAAAAAGAAA
1 AAGAAAAA-AAA
* *
1283807 AAG-AAAGAGA
1 AAGAAAAAAAA
1283817 AAGAAAAAAAA
1 AAGAAAAAAAA
1283828 AAGAAAAAA
1 AAGAAAAAA
1283837 GTATGAAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 5 0.14
11 25 0.71
12 5 0.14
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:1283844 original size:22 final size:22
Alignment explanation
Indices: 1283784--1283835 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
1283774 TCCTCTAAAT
*
1283784 AAGAAAAACAAAAGAAAAAGAAA
1 AAGAAAAA-GAAAGAAAAAGAAA
*
1283807 AAGAAAGAGAAAGAAAAA-AAA
1 AAGAAAAAGAAAGAAAAAGAAA
1283828 AAGAAAAA
1 AAGAAAAA
1283836 AGTATGAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 10 0.38
22 9 0.35
23 7 0.27
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (22 bp):
AAGAAAAAGAAAGAAAAAGAAA
Found at i:1285176 original size:44 final size:43
Alignment explanation
Indices: 1285128--1285270 Score: 121
Period size: 44 Copynumber: 3.3 Consensus size: 43
1285118 ATGCTCATAA
1285128 TTGTGTCATTTCACGCACATTTGTAGTTTTGATAACATTTGCAT
1 TTGTGTCATTTCACGCACATTTGTA-TTTTGATAACATTTGCAT
* ** * **
1285172 TTGTGTCATTTCATGTGCATTTGCTATTTT-ATTGATC-CCTGCAT
1 TTGTGTCATTTCACGCACATTTG-TATTTTGA-T-AACATTTGCAT
* * * *
1285216 TTGCGTCATTTCAC-CTACATTTGCATTTTAGATAACATTGGTAT
1 TTGTGTCATTTCACGC-ACATTTGTATTTT-GATAACATTTGCAT
1285260 TTGTGTCATTT
1 TTGTGTCATTT
1285271 TATAGGCATT
Statistics
Matches: 75, Mismatches: 17, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
43 8 0.11
44 62 0.83
45 5 0.07
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.48
Consensus pattern (43 bp):
TTGTGTCATTTCACGCACATTTGTATTTTGATAACATTTGCAT
Found at i:1285195 original size:88 final size:87
Alignment explanation
Indices: 1285092--1285316 Score: 244
Period size: 88 Copynumber: 2.6 Consensus size: 87
1285082 TCATGCATAT
* * *
1285092 TTTCATTTGCATTTGCCCTTTTATTGATGCT-CATAATTGTGTCATTTCACGC-ACATTTGTAGT
1 TTTCATGTGCATTTGCCCTTTTATTGATGCTGCAT--TTGCGTCATTTCAC-CTACATTTGCA-T
*
1285155 TTT-GATAACATTTGCATTTGTGTCA
62 TTTAGATAACATTGGCATTTGTGTCA
** *
1285180 TTTCATGTGCATTTGCTATTTTATTGATCCCTGCATTTGCGTCATTTCACCTACATTTGCATTTT
1 TTTCATGTGCATTTGCCCTTTTATTGAT-GCTGCATTTGCGTCATTTCACCTACATTTGCATTTT
*
1285245 AGATAACATTGGTATTTGTGTCA
65 AGATAACATTGGCATTTGTGTCA
* * *
1285268 TTTTATAG-GCATTTGCCAC-TTTATTGATGCTTGCATTTGCATCGTTTCA
1 TTTCAT-GTGCATTTGCC-CTTTTATTGATGC-TGCATTTGCGTCATTTCA
1285317 TGCATATCTT
Statistics
Matches: 116, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
87 6 0.05
88 104 0.90
89 3 0.03
90 3 0.03
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.47
Consensus pattern (87 bp):
TTTCATGTGCATTTGCCCTTTTATTGATGCTGCATTTGCGTCATTTCACCTACATTTGCATTTTA
GATAACATTGGCATTTGTGTCA
Found at i:1285763 original size:89 final size:89
Alignment explanation
Indices: 1285617--1285823 Score: 197
Period size: 89 Copynumber: 2.3 Consensus size: 89
1285607 CAGCCCTTAG
* **
1285617 ATGGTATTGATGCATCACAAAGCTTGATTTCCTGGGGGCAAGATGCAACCAACACATTCCCAATC
1 ATGGTATTGATGCATCACAAAGCTTGA-TCCCTGGGAACAAGATGCAACCAACACATTCCCAATC
*
1285682 ATATTCC-C-TTCA-CTCAACCAGTAA
65 ATA-TCCTCTTTCACCT-AACCACTAA
* * * * * **
1285706 ATGGTATTGATGCATCACAAAGCTTGATCCCAT-GGAACAAAGGTGTAGCCCATACATTCTTAAT
1 ATGGTATTGATGCATCACAAAGCTTGATCCC-TGGGAAC-AAGATGCAACCAACACATTCCCAAT
* * *
1285770 CATATCCTCTTTTACCTAATCACTAG
64 CATATCCTCTTTCACCTAACCACTAA
* *
1285796 ATGGTATTAATGCATCACAAAGTTTGAT
1 ATGGTATTGATGCATCACAAAGCTTGAT
1285824 TTCCTTAGGG
Statistics
Matches: 97, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
88 9 0.09
89 51 0.53
90 35 0.36
91 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (89 bp):
ATGGTATTGATGCATCACAAAGCTTGATCCCTGGGAACAAGATGCAACCAACACATTCCCAATCA
TATCCTCTTTCACCTAACCACTAA
Found at i:1285823 original size:90 final size:89
Alignment explanation
Indices: 1285706--1285908 Score: 218
Period size: 90 Copynumber: 2.3 Consensus size: 89
1285696 CAACCAGTAA
* * ** *
1285706 ATGGTATTGATGCATCACAAAGCTTGA-TCCCAT-GGAACAAAGGTGTAGCCCATACATTCTTAA
1 ATGGTATTAATGCATCACAAAGTTTGATTCCCATAGG-AC-AAGGTAAAGCCCACACATTCTTAA
1285769 TCATATCCTCTTTTACCTAA-TCACTAG
64 TCATATCC-CTTTTACCTAACT-ACTAG
* * * * *
1285796 ATGGTATTAATGCATCACAAAGTTTGATTTCCTTAGGGCCAGGTAAAGCCCACAGATTCTTAATC
1 ATGGTATTAATGCATCACAAAGTTTGATTCCCATAGGACAAGGTAAAGCCCACACATTCTTAATC
*
1285861 ATATCCCTTTTATCTAACTACTAG
66 ATATCCCTTTTACCTAACTACTAG
* *
1285885 ATAGTACTAATGCATCA-AAA-TTTG
1 ATGGTATTAATGCATCACAAAGTTTG
1285909 TCTATCTTGG
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
87 4 0.04
88 3 0.03
89 30 0.31
90 53 0.55
91 5 0.05
92 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (89 bp):
ATGGTATTAATGCATCACAAAGTTTGATTCCCATAGGACAAGGTAAAGCCCACACATTCTTAATC
ATATCCCTTTTACCTAACTACTAG
Found at i:1286141 original size:48 final size:48
Alignment explanation
Indices: 1286065--1286206 Score: 184
Period size: 48 Copynumber: 3.0 Consensus size: 48
1286055 TTGATTGTAT
*
1286065 CTAGTCAAACTCTTTTCATCCCAT-GTTTGACTACT-TTGGTGTTAGGGC
1 CTAGTCAAACTCTTTTCAT-CCATCGTTTGACTA-TATTAGTGTTAGGGC
1286113 CT-GATCAAACTCTTTTCATCTC-TCGTTTGACTATATTAGTGTTAGGGC
1 CTAG-TCAAACTCTTTTCATC-CATCGTTTGACTATATTAGTGTTAGGGC
* * *
1286161 CTAGTCAAACTCTTTTCATCCTTCATTTGACTATATTAGTATTAGG
1 CTAGTCAAACTCTTTTCATCCATCGTTTGACTATATTAGTGTTAGG
1286207 ACCTGGTTAA
Statistics
Matches: 85, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
47 5 0.06
48 79 0.93
49 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.42
Consensus pattern (48 bp):
CTAGTCAAACTCTTTTCATCCATCGTTTGACTATATTAGTGTTAGGGC
Found at i:1286570 original size:42 final size:44
Alignment explanation
Indices: 1286509--1287211 Score: 204
Period size: 42 Copynumber: 16.7 Consensus size: 44
1286499 TTTAACTTCT
* * * *
1286509 TTACCTTC-AAGTCTACCTATTAGCTTTGACCTTAGAGGCTTTA
1 TTACCTTCTTAGTCTGCCTATCAGCTTTGACCTTAGAGACTTTA
* * *
1286552 TTA-CTT-TTAGTCTGCCTATCGGTTTTGACCTTAGAGACTTTC
1 TTACCTTCTTAGTCTGCCTATCAGCTTTGACCTTAGAGACTTTA
* * * *
1286594 TTACCTTCTTAGTCTGCCTGTCGGCTTTGACCCTAAAGACTTCT-
1 TTACCTTCTTAGTCTGCCTATCAGCTTTGACCTTAGAGACTT-TA
* * * ** *
1286638 TCACCTTC--AATCTACCTATTGGCTTTGACCTTAGAGA-TTTCC
1 TTACCTTCTTAGTCTGCCTATCAGCTTTGACCTTAGAGACTTT-A
* * * * **
1286680 TCACCTTC--AGTCTGCCTGTCAGTTTTGACCTTGGAGACTTCC
1 TTACCTTCTTAGTCTGCCTATCAGCTTTGACCTTAGAGACTTTA
* * * * * *
1286722 TTACCTT-TAAGTCTGCCTGTCAACATTGATCC-TGGAGAATTCT-
1 TTACCTTCTTAGTCTGCCTATCAGCTTTGA-CCTTAGAGACTT-TA
* * * * **
1286765 TCACCTTC--AGTCTACCTGTCAACTTTGA---T----ACTTCC
1 TTACCTTCTTAGTCTGCCTATCAGCTTTGACCTTAGAGACTTTA
* * * * *
1286800 TTACAC-TC-AAGTCTGCCTATCGGCTTTAACCCT-GAAGACTTCA
1 TTAC-CTTCTTAGTCTGCCTATCAGCTTTGACCTTAG-AGACTTTA
* * * * * *
1286843 TTACC-T-TTACTTTGCCCATCGGCTTTGACCTTGGAGACTTCA
1 TTACCTTCTTAGTCTGCCTATCAGCTTTGACCTTAGAGACTTTA
* * **
1286885 TTACC-T-TTAGTCTGCCTATCGGCTTTGACCTTAGAGGCTTCC
1 TTACCTTCTTAGTCTGCCTATCAGCTTTGACCTTAGAGACTTTA
* * * * * * * *
1286927 TTACC-T-TTAGTCTTCCTGTCAGTTTTCACCCTAAAAACTTCA
1 TTACCTTCTTAGTCTGCCTATCAGCTTTGACCTTAGAGACTTTA
* * * * * *
1286969 TTA---TCTTAAGTCTGCTTGTC-GACTTTCACCCTGGAGA-TTTCC
1 TTACCTTCTT-AGTCTGCCTATCAG-CTTTGACCTTAGAGACTTT-A
* *
1287011 TTACC-T-TTAGTTTGCCTATC-GACTTTGACCTT-GAAGACTTTT
1 TTACCTTCTTAGTCTGCCTATCAG-CTTTGACCTTAG-AGACTTTA
* * * * * * **
1287053 TTACCTTCTTAGTCTACCTGTCGGCTTTTACCCTGGAGACTTCC
1 TTACCTTCTTAGTCTGCCTATCAGCTTTGACCTTAGAGACTTTA
* * * *
1287097 TTACCCTC-AAGTCTGCCTAT-TGACTTTGACCCTAGAGACTTCT-
1 TTACCTTCTTAGTCTGCCTATCAG-CTTTGACCTTAGAGACTT-TA
* * *
1287140 TTACC-T-TTAGTCTGTCTGTC-GTCTTTGACCTTAGAGACTTTC
1 TTACCTTCTTAGTCTGCCTATCAG-CTTTGACCTTAGAGACTTTA
* *
1287182 TTACC-T-TTAGTCTGCCTGTTAGCTTTGACC
1 TTACCTTCTTAGTCTGCCTATCAGCTTTGACC
1287212 CTGGAGCTAG
Statistics
Matches: 516, Mismatches: 102, Indels: 85
0.73 0.15 0.12
Matches are distributed among these distances:
35 8 0.02
36 16 0.03
39 2 0.00
40 2 0.00
41 9 0.02
42 318 0.62
43 86 0.17
44 72 0.14
45 3 0.01
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.39
Consensus pattern (44 bp):
TTACCTTCTTAGTCTGCCTATCAGCTTTGACCTTAGAGACTTTA
Found at i:1286664 original size:128 final size:127
Alignment explanation
Indices: 1286503--1286781 Score: 344
Period size: 128 Copynumber: 2.2 Consensus size: 127
1286493 AACCTTTTTA
* * * * *
1286503 ACTTCTTTACCTTCAAGTCTACCTATTAGCTTTGACCTTAGAGGCTTT-ATTACTTTTAGTCTGC
1 ACTTCTTCACCTTCAA-TCTACCTATTAGCTTTGACCTTAGA-GATTTCATCACCTTCAGTCTGC
* * * ** *
1286567 CTATCGGTTTTGACCTTAGAGACTTTCTTACCTTCTTAGTCTGCCTGTCGGCTTTGACCCTAAAG
64 CTATCAGTTTTGACCTTAGAGACTTCCTTACCTT-TAAGTCTGCCTGTCAACATTGACCCTAAAG
* *
1286632 ACTTCTTCACCTTCAATCTACCTATTGGCTTTGACCTTAGAGATTTCCTCACCTTCAGTCTGCCT
1 ACTTCTTCACCTTCAATCTACCTATTAGCTTTGACCTTAGAGATTTCATCACCTTCAGTCTGCCT
* * * **
1286697 GTCAGTTTTGACCTTGGAGACTTCCTTACCTTTAAGTCTGCCTGTCAACATTGATCCTGGAG
66 ATCAGTTTTGACCTTAGAGACTTCCTTACCTTTAAGTCTGCCTGTCAACATTGACCCTAAAG
* *
1286759 AATTCTTCACCTTCAGTCTACCT
1 ACTTCTTCACCTTCAATCTACCT
1286782 GTCAACTTTG
Statistics
Matches: 129, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
127 48 0.37
128 66 0.51
129 15 0.12
ACGTcount: A:0.19, C:0.27, G:0.15, T:0.39
Consensus pattern (127 bp):
ACTTCTTCACCTTCAATCTACCTATTAGCTTTGACCTTAGAGATTTCATCACCTTCAGTCTGCCT
ATCAGTTTTGACCTTAGAGACTTCCTTACCTTTAAGTCTGCCTGTCAACATTGACCCTAAAG
Found at i:1286719 original size:84 final size:85
Alignment explanation
Indices: 1286566--1287213 Score: 282
Period size: 84 Copynumber: 7.7 Consensus size: 85
1286556 TTTTAGTCTG
* * *
1286566 CCTATCGGTTTTGACCTTAGAGACTTTCTTACCTTCTTAGTCTGCCTGTCGGCTTTGACCCTAAA
1 CCTATCGGCTTTGACCTTAGAGACTTTCTCACCTTC-TAGTCTGCCTGTCAGCTTTGACCCTAAA
1286631 GACTT-CTTCACCTTCAATCTA
65 GACTTCCTT-ACCTTCAATCTA
* * * **
1286652 CCTATTGGCTTTGACCTTAGAGA-TTTCCTCACCTTC-AGTCTGCCTGTCAGTTTTGACCTTGGA
1 CCTATCGGCTTTGACCTTAGAGACTTT-CTCACCTTCTAGTCTGCCTGTCAGCTTTGACCCTAAA
* *
1286715 GACTTCCTTACCTTTAAGTCTG
65 GACTTCCTTACCTTCAA-TCTA
* ** * * * * *
1286737 CCTGTCAACATTGATCC-TGGAGA-ATTCTTCACCTTC-AGTCTACCTGTCAACTTTGA---T--
1 CCTATCGGCTTTGA-CCTTAGAGACTTTC-TCACCTTCTAGTCTGCCTGTCAGCTTTGACCCTAA
*
1286794 --ACTTCCTTACAC-TCAAGTCTG
64 AGACTTCCTTAC-CTTCAA-TCTA
* * * * * ** * * **
1286815 CCTATCGGCTTTAACCCT-GAAGAC-TTCATTACCTT-TACTTTGCCCATCGGCTTTGACCTTGG
1 CCTATCGGCTTTGACCTTAG-AGACTTTC-TCACCTTCTAGTCTGCCTGTCAGCTTTGACCCTAA
* * * *
1286877 AGACTTCATTACCTTTAGTCTG
64 AGACTTCCTTACCTTCAATCTA
* * * * * * *
1286899 CCTATCGGCTTTGACCTTAGAGGCTTCCTTACCTT-TAGTCTTCCTGTCAGTTTTCACCCTAAAA
1 CCTATCGGCTTTGACCTTAGAGACTTTCTCACCTTCTAGTCTGCCTGTCAGCTTTGACCCTAAAG
* * *
1286963 ACTTCATTATCTT-AAGTCTG
66 ACTTCCTTACCTTCAA-TCTA
* * * * * * * * * * *
1286983 CTTGTCGACTTTCACCCTGGAGA-TTTCCTTACCTT-TAGTTTGCCTATC-GACTTTGACCTTGA
1 CCTATCGGCTTTGACCTTAGAGACTTT-CTCACCTTCTAGTCTGCCTGTCAG-CTTTGACCCTAA
** *
1287045 AGACTTTTTTACCTTCTTAGTCTA
64 AGACTTCCTTACCTTC--AATCTA
* * * * * * * * * * *
1287069 CCTGTCGGCTTTTACCCTGGAGACTTCCTTACCCTCAAGTCTGCCTAT-TGACTTTGACCCTAGA
1 CCTATCGGCTTTGACCTTAGAGACTTTCTCACCTTCTAGTCTGCCTGTCAG-CTTTGACCCTAAA
* * * *
1287133 GACTTCTTTACCTTTAGTCTG
65 GACTTCCTTACCTTCAATCTA
* * * * *
1287154 TCTGTCGTCTTTGACCTTAGAGACTTTCTTACCTT-TAGTCTGCCTGTTAGCTTTGACCCT
1 CCTATCGGCTTTGACCTTAGAGACTTTCTCACCTTCTAGTCTGCCTGTCAGCTTTGACCCT
1287214 GGAGCTAGAG
Statistics
Matches: 432, Mismatches: 100, Indels: 62
0.73 0.17 0.10
Matches are distributed among these distances:
77 3 0.01
78 53 0.12
79 1 0.00
81 1 0.00
82 1 0.00
83 4 0.01
84 172 0.40
85 98 0.23
86 61 0.14
87 38 0.09
ACGTcount: A:0.18, C:0.28, G:0.15, T:0.39
Consensus pattern (85 bp):
CCTATCGGCTTTGACCTTAGAGACTTTCTCACCTTCTAGTCTGCCTGTCAGCTTTGACCCTAAAG
ACTTCCTTACCTTCAATCTA
Found at i:1287223 original size:48 final size:49
Alignment explanation
Indices: 1287171--1287266 Score: 122
Period size: 49 Copynumber: 2.0 Consensus size: 49
1287161 TCTTTGACCT
** *
1287171 TAGAGACTTTCTTA-CCTTTAGTCTGCCTGTTAGCTTTGACCCTGGAGC
1 TAGAGACTTTCTTACCCTCAAGTCTGCCTGTCAGCTTTGACCCTGGAGC
* * * *
1287219 TAGAGAGTTTTTTACCCTCAAGTTTGCCTGTCAGCTTTGACCTTGGAG
1 TAGAGACTTTCTTACCCTCAAGTCTGCCTGTCAGCTTTGACCCTGGAG
1287267 ACTTCCTTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
48 12 0.30
49 28 0.70
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.38
Consensus pattern (49 bp):
TAGAGACTTTCTTACCCTCAAGTCTGCCTGTCAGCTTTGACCCTGGAGC
Done.