Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008953.1 Hibiscus syriacus cultivar Beakdansim tig00112281_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2822058
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 15
Found at i:1102868 original size:39 final size:38
Alignment explanation
Indices: 1102801--1102878 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 38
1102791 AAATGAATTG
* *
1102801 AAAAAAATAAATAAAAAATAAAACAAAATAAGTCAAAGA
1 AAAAAAATAAATAAAAAAGAAAAAAAAAT-AGTCAAAGA
*
1102840 AAAAAAATAAA-AAAAAAGAAATAAAAAATATTCAAAGA
1 AAAAAAATAAATAAAAAAGAAA-AAAAAATAGTCAAAGA
1102878 A
1 A
1102879 CATAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
38 18 0.51
39 17 0.49
ACGTcount: A:0.78, C:0.04, G:0.05, T:0.13
Consensus pattern (38 bp):
AAAAAAATAAATAAAAAAGAAAAAAAAATAGTCAAAGA
Found at i:1104092 original size:13 final size:14
Alignment explanation
Indices: 1104064--1104093 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1104054 TATTAGTTTA
1104064 ATAACAACAGTAAT
1 ATAACAACAGTAAT
1104078 ATAACAACA-TAAT
1 ATAACAACAGTAAT
1104091 ATA
1 ATA
1104094 CATACTATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.60, C:0.13, G:0.03, T:0.23
Consensus pattern (14 bp):
ATAACAACAGTAAT
Found at i:1104769 original size:84 final size:84
Alignment explanation
Indices: 1104661--1104817 Score: 226
Period size: 84 Copynumber: 1.9 Consensus size: 84
1104651 TTTTATTGAC
** *
1104661 AGATAGCCCTTCTTGCCTCGAGCTATGCTGTAAATGATGTGCCCTTGAGCTTAGTGTAAT-CGAA
1 AGATAGCCCTTCTTGCCTCGAGCTATGCTACAAATGATGTGCCCTTGAGCTGAGTGT-ATCCGAA
1104725 CTGGAAGGTATTTGGTCGGA
65 CTGGAAGGTATTTGGTCGGA
* * * *
1104745 AGATAGCCCTTCTTTCCTTGAGCTATGCTACAAATGATGTTCCTTTGAGCTGAGTGTATCCGAAC
1 AGATAGCCCTTCTTGCCTCGAGCTATGCTACAAATGATGTGCCCTTGAGCTGAGTGTATCCGAAC
*
1104810 TTGAAGGT
66 TGGAAGGT
1104818 TTGGTGTTTC
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
83 2 0.03
84 62 0.97
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (84 bp):
AGATAGCCCTTCTTGCCTCGAGCTATGCTACAAATGATGTGCCCTTGAGCTGAGTGTATCCGAAC
TGGAAGGTATTTGGTCGGA
Found at i:1104900 original size:37 final size:36
Alignment explanation
Indices: 1104859--1104943 Score: 134
Period size: 37 Copynumber: 2.3 Consensus size: 36
1104849 TTTTTTTGTG
1104859 TGTTTCAAGAGAAACTGTATCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTATCAAGAGAGACAAAA-TT
* * *
1104896 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTATCAAGAGAGACAAAATT
1104932 TGTTTCAAGAGA
1 TGTTTCAAGAGA
1104944 GACAAAACTT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 13 0.30
37 31 0.70
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTATCAAGAGAGACAAAATT
Found at i:1104939 original size:21 final size:21
Alignment explanation
Indices: 1104878--1104950 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
1104868 AGAAACTGTA
1104878 TCAAGAGAGACAAAACTTTGTT
1 TCAAGAGAGACAAAA-TTTGTT
*
1104900 TCAAG-G-G---AAA-TTGTC
1 TCAAGAGAGACAAAATTTGTT
1104915 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
1104936 TCAAGAGAGACAAAA
1 TCAAGAGAGACAAAA
1104951 CTTAGTTCCA
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
15 9 0.21
16 1 0.02
17 4 0.09
20 4 0.09
21 20 0.47
22 5 0.12
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:1104942 original size:58 final size:58
Alignment explanation
Indices: 1104878--1105066 Score: 193
Period size: 58 Copynumber: 3.1 Consensus size: 58
1104868 AGAAACTGTA
*
1104878 TCAAGAGAGACAAAACTTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
* * ** * *
1104936 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGGGAGACAAAATTTGTT
1 TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
* * *
1104994 T-AATGTAAAACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATATTT-
1 TCAA-G----AGAGA--CAAA-ACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA-ATTTG
1105057 TT
57 TT
1105059 TCAAGAGA
1 TCAAGAGA
1105067 ATCTGCCTAT
Statistics
Matches: 104, Mismatches: 17, Indels: 17
0.75 0.12 0.12
Matches are distributed among these distances:
57 2 0.02
58 53 0.51
61 2 0.02
62 3 0.03
64 4 0.04
65 34 0.33
66 6 0.06
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.28
Consensus pattern (58 bp):
TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
Found at i:1105091 original size:138 final size:138
Alignment explanation
Indices: 1104936--1105270 Score: 455
Period size: 138 Copynumber: 2.4 Consensus size: 138
1104926 AAAATTTGTT
* *
1104936 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGGGAGACAAAATTTGTTT-AATGT
1 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAA-GG
*
1105000 AAAACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATATTT-TTTCAAG
65 AAAACATATTCAAAGATTTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAA-ATTTGTTTCAAG
*
1105064 AGAATCTGCC
129 AGAAACTGCC
* * *
1105074 T-ATAGAGAGACAAAACTTAGTTCCAAAAGAATCTGTCTCAAAGGAGATGAAAA-TTGTTTCAAG
1 TCA-AGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGA-CAAAATTTGTTTCAAG
*
1105137 GAAAACATATTCAAAGATTTTATTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAG
64 GAAAACATATTCAAAGATTTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG
* *
1105202 GGAAACTGTC
129 AGAAACTGCC
* * * * *
1105212 TCAAGGGAGACAAAATTTA-TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
1 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTT
1105271 TGAGTAAATT
Statistics
Matches: 172, Mismatches: 18, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
136 4 0.02
137 27 0.16
138 134 0.78
139 7 0.04
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.27
Consensus pattern (138 bp):
TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGA
AAACATATTCAAAGATTTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAG
AAACTGCC
Found at i:1105206 original size:36 final size:36
Alignment explanation
Indices: 1105159--1105270 Score: 179
Period size: 36 Copynumber: 3.1 Consensus size: 36
1105149 AAAGATTTTA
*
1105159 TTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
* *
1105195 TTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
*
1105231 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTG
1105268 TTT
1 TTT
1105271 TGAGTAAATT
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
36 63 0.91
37 6 0.09
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (36 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
Found at i:1108541 original size:21 final size:21
Alignment explanation
Indices: 1108502--1108541 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1108492 AGTTAGTGAG
* **
1108502 ATAATGATAATAATCAAAACA
1 ATAATGAAAATAAAAAAAACA
1108523 ATAATGAAAATAAAAAAAA
1 ATAATGAAAATAAAAAAAA
1108542 TCATACCCCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (21 bp):
ATAATGAAAATAAAAAAAACA
Found at i:1109462 original size:6 final size:7
Alignment explanation
Indices: 1109446--1109483 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
1109436 CTTAGTTGCG
1109446 AAAATTT
1 AAAATTT
1109453 AAAA-TT
1 AAAATTT
1109459 AAAATTT
1 AAAATTT
1109466 AAAA-TT
1 AAAATTT
1109472 AAAATTT
1 AAAATTT
1109479 AAAAT
1 AAAAT
1109484 ATTCGATTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 12 0.41
7 17 0.59
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (7 bp):
AAAATTT
Found at i:1109464 original size:13 final size:13
Alignment explanation
Indices: 1109446--1109483 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
1109436 CTTAGTTGCG
1109446 AAAATTTAAAATT
1 AAAATTTAAAATT
1109459 AAAATTTAAAATT
1 AAAATTTAAAATT
1109472 AAAATTTAAAAT
1 AAAATTTAAAAT
1109484 ATTCGATTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAATTTAAAATT
Found at i:1112637 original size:84 final size:84
Alignment explanation
Indices: 1112395--1113350 Score: 1007
Period size: 84 Copynumber: 11.4 Consensus size: 84
1112385 TTTTTATTGA
* * * * * * * * *
1112395 CAGATAGCCTTTCTTGCCTTGAGCTAAGCTGTAAATGATGTGCCTTTGAGCCGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * *
1112460 CTCAAAGGTC-TTTGTTGA
66 CTCGAAGGTCTTTTGGTGG
* * * * * * *
1112478 CAAATAACCTTTCTAGCCTTTAGTTATGCTGTAAATGATGTGCCCTT--AGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
*
1112541 ACTCGTAGGTCTTTTGGTGG
65 ACTCGAAGGTCTTTTGGTGG
* * * *
1112561 CAGATAGCCCTTCTAGCCTTGAGCTATACTGCAAATGATGTGCCTTGGAGCTGAACGTTGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
1112626 CTCGAAGGTC-TTTGGTTGA
66 CTCGAAGGTCTTTTGG-TGG
** * *
1112645 CAGATAACCCTTCTAGCCTTGATTTATGCTGCAAATGATATGCCTTGGAGCTGGGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * **
1112710 TTCGAATGTCGTTTGGTAA
66 CTCGAAGGTCTTTTGGTGG
* * * * * *
1112729 CAAATAACCCTTATTGCCTTGAGCTATGCTGCAAATAATGTACCTTGGAGCTGAGCGTAGTCGAG
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1112794 CTCGAAGGTC-TTTGGTTGG
66 CTCGAAGGTCTTTTGG-TGG
* * * *
1112813 CAGATAACCCTTCTAGCCTTGAGTTATGATGCAAATGATATGCCTTGGAGCTGAGCGTAGTTGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
1112878 CTTGAAGGTCGTTTGGTGG
66 CTCGAAGGTCTTTTGGTGG
* * * * * * * *
1112897 TAGATAGCCCTTCTAGCCTTAAGTTATACTGTAAATGATGTTCCTTGGAGCTGAGCGTAGCCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
1112962 CTCGAAGGT-ATTTGGTTGG
66 CTCGAAGGTCTTTTGG-TGG
* * * * *
1112981 CAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATAATGTGCCTT--A-CTAAGTGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1113043 CTCGAAGGTCTTTTGGTGG
66 CTCGAAGGTCTTTTGGTGG
* * *
1113062 TAGATAACCCTTCTAGCTTTGAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
1113127 CTCGAAGGTCTTTTGTTGG
66 CTCGAAGGTCTTTTGGTGG
*
1113146 CAGATAACCCTTCTAGTCCTTGAG-TAATGCTGCAAATGATGTGACTTGGAGCTGAGCGTAGTCG
1 CAGATAACCCTTCTAG-CCTTGAGCT-ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCG
* *
1113210 AACTCGAATGTCTTTTGTTGG
64 AACTCGAAGGTCTTTTGGTGG
* * * * * * * * * * *
1113231 AAGATAGCCTTTCTCGCCTTGAGCTATACTGCAAATGTTATGCCTTTGAGCTGAGTGTAATTGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* **
1113296 CTCGATGGTCTTTTATTGG
66 CTCGAAGGTCTTTTGGTGG
* * * *
1113315 TAGATAACCCTT-TTGACCTTGAGTTATGCTACAAAT
1 CAGATAACCCTTCTAG-CCTTGAGCTATGCTGCAAAT
1113351 AGTTTCTTTA
Statistics
Matches: 737, Mismatches: 119, Indels: 33
0.83 0.13 0.04
Matches are distributed among these distances:
81 65 0.09
82 34 0.05
83 95 0.13
84 458 0.62
85 85 0.12
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.33
Consensus pattern (84 bp):
CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTTGGTGG
Found at i:1112782 original size:168 final size:168
Alignment explanation
Indices: 1112395--1113350 Score: 1116
Period size: 168 Copynumber: 5.7 Consensus size: 168
1112385 TTTTTATTGA
* * * * * * * * *
1112395 CAGATAGCCTTTCTTGCCTTGAGCTAAGCTGTAAATGATGTGCCTTTGAGCCGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * * * *
1112460 CTCAAAGGTCTTT-GTTGACAAATAACCTTTCTAGCCTTTAGTTATGCTGTAAATGATGTGCCCT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG-CCT
* * *
1112524 T--AGCTGAGTGTAATCGAACTCGTAGGTCTTTTGGTGG
130 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGG
* * * *
1112561 CAGATAGCCCTTCTAGCCTTGAGCTATACTGCAAATGATGTGCCTTGGAGCTGAACGTTGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * *
1112626 CTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGCCTTGATTTATGCTGCAAATGATATGCCTT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTT
* * * * **
1112691 GGAGCTGGGCGTAGTCGAATTCGAATGTCGTTTGGTAA
131 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGG
* * * * * *
1112729 CAAATAACCCTTATTGCCTTGAGCTATGCTGCAAATAATGTACCTTGGAGCTGAGCGTAGTCGAG
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
1112794 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGATGCAAATGATATGCCTT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTT
* * *
1112859 GGAGCTGAGCGTAGTTGAACTTGAAGGTCGTTTGGTGG
131 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGG
* * * * * * * *
1112897 TAGATAGCCCTTCTAGCCTTAAGTTATACTGTAAATGATGTTCCTTGGAGCTGAGCGTAGCCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * *
1112962 CTCGAAGGTATTTGGTTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATAATGTGCCTT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTT
* *
1113027 --A-CTAAGTGTAGTCGAACTCGAAGGTCTTTTGGTGG
131 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGG
* * *
1113062 TAGATAACCCTTCTAGCTTTGAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * *
1113127 CTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGTCCTTGAGTAATGCTGCAAATGATGTGACT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAG-CCTTGAGTTATGCTGCAAATGATGTGCCT
* *
1113192 TGGAGCTGAGCGTAGTCGAACTCGAATGTCTTTTGTTGG
130 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGG
* * * * * * * * * * *
1113231 AAGATAGCCTTTCTCGCCTTGAGCTATACTGCAAATGTTATGCCTTTGAGCTGAGTGTAATTGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* ** * * *
1113296 CTCGATGGTCTTTTATTGGTAGATAACCCTT-TTGACCTTGAGTTATGCTACAAAT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAG-CCTTGAGTTATGCTGCAAAT
1113351 AGTTTCTTTA
Statistics
Matches: 675, Mismatches: 108, Indels: 12
0.85 0.14 0.02
Matches are distributed among these distances:
165 117 0.17
166 98 0.15
167 41 0.06
168 308 0.46
169 111 0.16
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.33
Consensus pattern (168 bp):
CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTT
GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGG
Found at i:1113322 original size:502 final size:502
Alignment explanation
Indices: 1112396--1113342 Score: 1292
Period size: 502 Copynumber: 1.9 Consensus size: 502
1112386 TTTTATTGAC
* * * * * *
1112396 AGATAGCCTTTCTTGCCTTGAGCTAAGCTGTAAATGATGTGCCTTTGAGCCGAGTGTAATCGAAC
1 AGATAGCCCTTCTAGCCTTAAGCTAAGCTGTAAATGATGTGCCTTGGAGCCGAGCGTAACCGAAC
* * * * *
1112461 TCAAAGGTCTTTGTTGACAAATAACCTTTCTAGCCTTTAGTTATGCTGTAAATGATGTGCCCTTA
66 TCAAAGGTATTTGTTGACAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATAATGTGCCCTTA
* * *
1112526 GCTGAGTGTAATCGAACTCGTAGGTCTTTTGGTGGCAGATAGCCCTTCTAGCCTTGAGCTATACT
131 GCTAAGTGTAATCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTAGCCTTGAGCTATACT
* *
1112591 GCAAATGATGTGCCTTGGAGCTGAACGTTGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCT
196 GCAAATGATGTGCCTTAGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCT
* * * * *
1112656 TCTAGCCTTGATTTATGCTGCAAATGATATGCCTTGGAGCTGGGCGTAGTCGAATTCGAATGTCG
261 TCTAGCCTTGAGTAATGCTGCAAATGATATGACTTGGAGCTGAGCGTAGTCGAACTCGAATGTCG
* * *
1112721 TTTGGTAACAAATAACCCTTATTGCCTTGAGCTATGCTGCAAATAATGTACCTTGGAGCTGAGCG
326 TTTGGTAACAAATAACCCTTATCGCCTTGAGCTATACTGCAAATAATATACCTTGGAGCTGAGCG
* * *
1112786 TAGTCGAGCTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAG-CCTTGAGTTATGATGCAAATG
391 TAATCGAACTCGAAGGTCTTTGATTGGCAGATAACCCTT-TAGACCTTGAGTTATGATGCAAATG
1112850 ATATGCCTTGGAGCTGAGCGTAGTTGAACTTGAAGGTCGTTTGGTGGT
455 ATATGCCTTGGAGCTGAGCGTAGTTGAACTTGAAGGTCGTTTGGTGGT
* * * *
1112898 AGATAGCCCTTCTAGCCTTAAGTTATA-CTGTAAATGATGTTCCTTGGAGCTGAGCGTAGCCGAA
1 AGATAGCCCTTCTAGCCTTAAGCTA-AGCTGTAAATGATGTGCCTTGGAGCCGAGCGTAACCGAA
* *
1112962 CTCGAAGGTATTTGGTTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATAATGTG-CCT
65 CTCAAAGGTATTT-GTTGACAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATAATGTGCCCT
* * * *
1113026 TA-CTAAGTGTAGTCGAACTCGAAGGTCTTTTGGTGGTAGATAACCCTTCTAGCTTTGAGCTATG
129 TAGCTAAGTGTAATCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTAGCCTTGAGCTATA
* * *
1113090 CTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACC
194 CTGCAAATGATGTGCCTTAGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACC
*
1113155 CTTCTAGTCCTTGAGTAATGCTGCAAATGATGTGACTTGGAGCTGAGCGTAGTCGAACTCGAATG
259 CTTCTAG-CCTTGAGTAATGCTGCAAATGATATGACTTGGAGCTGAGCGTAGTCGAACTCGAATG
* * * * * * * ** * *
1113220 TCTTTTGTTGGA-AGATAGCCTTTCTCGCCTTGAGCTATACTGCAAATGTTATGCCTTTGAGCTG
323 TCGTTTGGT-AACAAATAACCCTTATCGCCTTGAGCTATACTGCAAATAATATACCTTGGAGCTG
* * * * * *
1113284 AGTGTAATTGAACTCGATGGTCTTTTATTGGTAGATAACCCTTTTGACCTTGAGTTATG
387 AGCGTAATCGAACTCGAAGGTCTTTGATTGGCAGATAACCCTTTAGACCTTGAGTTATG
1113343 CTACAAATAG
Statistics
Matches: 382, Mismatches: 58, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
501 124 0.32
502 214 0.56
503 44 0.12
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.33
Consensus pattern (502 bp):
AGATAGCCCTTCTAGCCTTAAGCTAAGCTGTAAATGATGTGCCTTGGAGCCGAGCGTAACCGAAC
TCAAAGGTATTTGTTGACAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATAATGTGCCCTTA
GCTAAGTGTAATCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTAGCCTTGAGCTATACT
GCAAATGATGTGCCTTAGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCT
TCTAGCCTTGAGTAATGCTGCAAATGATATGACTTGGAGCTGAGCGTAGTCGAACTCGAATGTCG
TTTGGTAACAAATAACCCTTATCGCCTTGAGCTATACTGCAAATAATATACCTTGGAGCTGAGCG
TAATCGAACTCGAAGGTCTTTGATTGGCAGATAACCCTTTAGACCTTGAGTTATGATGCAAATGA
TATGCCTTGGAGCTGAGCGTAGTTGAACTTGAAGGTCGTTTGGTGGT
Found at i:1114683 original size:88 final size:88
Alignment explanation
Indices: 1114504--1114667 Score: 213
Period size: 88 Copynumber: 1.9 Consensus size: 88
1114494 ATTGTATAGA
* * *
1114504 TATTAGAATCACCTGTATCAGGCTAGTTGAATATTATCCATAAAGCCGAGGCGTTTAGCCAATTG
1 TATTAGAATCACCTGTATAAGGCTAGCTGAATATTATCCATAAAGCCGAGGCGTTTAACCAATTG
* *
1114569 CTCTAGAGGGACAACTAAAACTT
66 CTCTAAAGAGACAACTAAAACTT
* * * * *
1114592 TATTATAATCACCTTTATAAGGCTAGCTGAATCTTATCCATAAAGCTG-GAGCTTTTAACCAATT
1 TATTAGAATCACCTGTATAAGGCTAGCTGAATATTATCCATAAAGCCGAG-GCGTTTAACCAATT
*
1114656 GCTTTAAAGAGA
65 GCTCTAAAGAGA
1114668 TAGCTCAAGC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
87 1 0.02
88 63 0.98
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (88 bp):
TATTAGAATCACCTGTATAAGGCTAGCTGAATATTATCCATAAAGCCGAGGCGTTTAACCAATTG
CTCTAAAGAGACAACTAAAACTT
Found at i:1118345 original size:19 final size:21
Alignment explanation
Indices: 1118307--1118345 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
1118297 TCCAGTTGTC
*
1118307 TTTAATTAAGAAAATTATAAG
1 TTTAATTAAGAAAATGATAAG
1118328 TTTAATT-A-AAAATGATAA
1 TTTAATTAAGAAAATGATAA
1118346 AATAACGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 1 0.06
21 7 0.41
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (21 bp):
TTTAATTAAGAAAATGATAAG
Found at i:1119162 original size:20 final size:20
Alignment explanation
Indices: 1119100--1119369 Score: 269
Period size: 20 Copynumber: 13.5 Consensus size: 20
1119090 TGATTTTCCA
* ** *
1119100 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1119120 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1119140 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1119160 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1119180 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1119200 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1119220 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1119240 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1119260 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1119280 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1119300 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1119320 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1119340 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1119360 AAATCACAAC
1 AAATCGCAAC
1119370 ACTGAAATTT
Statistics
Matches: 210, Mismatches: 32, Indels: 16
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 206 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1120090 original size:24 final size:24
Alignment explanation
Indices: 1120051--1120097 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1120041 AAATTTGGTC
1120051 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1120075 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1120098 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1122567 original size:33 final size:34
Alignment explanation
Indices: 1122516--1122680 Score: 183
Period size: 33 Copynumber: 4.7 Consensus size: 34
1122506 CGGAAATTAC
* *
1122516 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
1122549 AATCCCAAC-ATGAAAATCGCAATGCAGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
1122583 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AATGAAAATCGCAATGCGAAATGAA
* *
1122621 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
1122654 AATCGCAATACGAAATGAAAATCGCAA
1 AATCGC-A-AC--AATGAAAATCGCAA
1122681 CGAGAGAATC
Statistics
Matches: 113, Mismatches: 7, Indels: 19
0.81 0.05 0.14
Matches are distributed among these distances:
32 1 0.01
33 48 0.42
34 17 0.15
35 2 0.02
36 2 0.02
37 1 0.01
38 26 0.23
39 16 0.14
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:1122599 original size:19 final size:19
Alignment explanation
Indices: 1122530--1122718 Score: 210
Period size: 19 Copynumber: 10.7 Consensus size: 19
1122520 GCAACGAGAG
1122530 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1122549 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1122563 AATCGCAATGCAGAAATGAA
1 AATCGCAATGC-GAAATGAA
1122583 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1122602 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1122621 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1122635 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1122654 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1122673 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
1122687 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
1122706 AATCGCATTGCGA
1 AATCGCAATGCGA
1122719 TTCTCCCGTT
Statistics
Matches: 145, Mismatches: 9, Indels: 32
0.78 0.05 0.17
Matches are distributed among these distances:
14 32 0.22
15 2 0.01
16 5 0.03
17 5 0.03
18 2 0.01
19 83 0.57
20 16 0.11
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1122657 original size:52 final size:52
Alignment explanation
Indices: 1122516--1122718 Score: 272
Period size: 52 Copynumber: 3.9 Consensus size: 52
1122506 CGGAAATTAC
*
1122516 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
1122563 AATCGCAATGCAGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
1122621 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATACGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
1122673 AATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCGA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1122719 TTCTCCCGTT
Statistics
Matches: 138, Mismatches: 7, Indels: 17
0.85 0.04 0.10
Matches are distributed among these distances:
47 8 0.06
49 1 0.01
50 1 0.01
52 83 0.60
53 29 0.21
55 2 0.01
56 1 0.01
58 13 0.09
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1122767 original size:19 final size:19
Alignment explanation
Indices: 1122727--1122824 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1122717 GATTCTCCCG
1122727 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1122747 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1122766 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1122780 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1122799 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1122818 TTGCGAT
1 TTGCGAT
1122825 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1122821 original size:52 final size:53
Alignment explanation
Indices: 1122708--1122824 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
1122698 GAAATTAAAA
1122708 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
1122761 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1122813 TCGCATTGCGAT
1 TCGCATTGCGAT
1122825 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1122950 original size:14 final size:14
Alignment explanation
Indices: 1122931--1122967 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1122921 CATCAATTAC
1122931 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1122945 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1122959 ACAAATCAA
1 ACAAATCAA
1122968 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1124906 original size:20 final size:19
Alignment explanation
Indices: 1124881--1125014 Score: 96
Period size: 19 Copynumber: 7.6 Consensus size: 19
1124871 TAGTTTACTT
*
1124881 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
*
1124901 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
*
1124920 TCGCAACGCGAAA-TGAAA
1 TCGCAACGCGAAACTAAAA
*
1124938 TCGCAA--CG--AC-AGAA
1 TCGCAACGCGAAACTAAAA
1124952 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
*
1124971 TCGCAA--CG-AA--AGAA
1 TCGCAACGCGAAACTAAAA
1124985 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
*
1125004 TCGCAATGCGA
1 TCGCAACGCGA
1125015 TTTTGGTTTC
Statistics
Matches: 92, Mismatches: 10, Indels: 25
0.72 0.08 0.20
Matches are distributed among these distances:
14 18 0.20
16 8 0.09
17 4 0.04
18 10 0.11
19 39 0.42
20 13 0.14
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:1124955 original size:14 final size:14
Alignment explanation
Indices: 1124936--1124992 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1124926 CGCGAAATGA
*
1124936 AATCGCAACGACAG
1 AATCGCAACGAAAG
1124950 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
1124967 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1124983 AATCGCAACG
1 AATCGCAACG
1124993 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1124975 original size:51 final size:47
Alignment explanation
Indices: 1124899--1124992 Score: 134
Period size: 51 Copynumber: 1.9 Consensus size: 47
1124889 CGAAACTTAA
1124899 AATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAATCGCAACGACAG
1 AATCGCAACGCGAAACCAAAATCGCAA--CGAAA-G-AATCGCAACGACAG
**
1124950 AATCGCAACGCGAAATGAAAATCGCAACGAAAGAATCGCAACG
1 AATCGCAACGCGAAACCAAAATCGCAACGAAAGAATCGCAACG
1124993 CGAAATGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
47 10 0.24
48 1 0.02
49 5 0.12
51 25 0.61
ACGTcount: A:0.46, C:0.26, G:0.20, T:0.09
Consensus pattern (47 bp):
AATCGCAACGCGAAACCAAAATCGCAACGAAAGAATCGCAACGACAG
Found at i:1124977 original size:33 final size:33
Alignment explanation
Indices: 1124918--1125009 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1124908 GCGAAACCAA
*
1124918 AATCGCAACGCGAAATG-AAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1124950 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1124983 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1125010 TGCGATTTTG
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 17 0.29
33 41 0.71
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1125032 original size:19 final size:19
Alignment explanation
Indices: 1125010--1125138 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1125000 AAAATCGCAA
1125010 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1125029 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1125043 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1125062 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1125076 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1125095 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1125114 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1125134 TGCGA
1 TGCGA
1125139 AGTAAACTAT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1125052 original size:33 final size:33
Alignment explanation
Indices: 1125010--1125101 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1125000 AAAATCGCAA
1125010 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1125043 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1125076 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1125102 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1125326 original size:93 final size:93
Alignment explanation
Indices: 1125185--1125837 Score: 1276
Period size: 93 Copynumber: 7.1 Consensus size: 93
1125175 ATGGATTGCA
1125185 TTAC-TTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1125248 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1125276 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1125341 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1125369 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1125434 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1125462 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1125527 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1125555 TTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1125619 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1125647 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1125712 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1125740 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1125805 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1125833 TTACT
1 TTACT
1125838 AAGCAATCTA
Statistics
Matches: 558, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
91 4 0.01
92 111 0.20
93 443 0.79
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1125686 original size:278 final size:279
Alignment explanation
Indices: 1125185--1125837 Score: 1276
Period size: 278 Copynumber: 2.4 Consensus size: 279
1125175 ATGGATTGCA
1125185 TTAC-TTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1125248 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
1125313 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
1125378 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
196 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
1125443 TGGCAGCAACCGAACAAAT
261 TGGCAGCAACCGAACAAAT
1125462 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1125527 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC-AAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
1125591 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
1125656 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
196 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
1125721 TGGCAGCAACCGAACAAAT
261 TGGCAGCAACCGAACAAAT
1125740 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1125805 TAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACT
1125838 AAGCAATCTA
Statistics
Matches: 373, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
277 4 0.01
278 277 0.74
279 92 0.25
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (279 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
TGGCAGCAACCGAACAAAT
Found at i:1127561 original size:14 final size:14
Alignment explanation
Indices: 1127542--1127631 Score: 54
Period size: 14 Copynumber: 5.7 Consensus size: 14
1127532 TTGAAATGAA
1127542 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1127556 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1127575 AATCGCAACTAGAG
1 AATCGCAACGAGAG
*
1127589 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1127608 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1127622 AATCACAACG
1 AATCGCAACG
1127632 CGAAATGAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 29 0.49
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 20 0.34
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1127574 original size:33 final size:33
Alignment explanation
Indices: 1127534--1127641 Score: 198
Period size: 33 Copynumber: 3.3 Consensus size: 33
1127524 TCTTTTGGTT
1127534 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1127567 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1127600 GAAATGAAAATCGCAACGAGAGAATCACAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1127633 GAAATGAAA
1 GAAATGAAA
1127642 TCACAATGCG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.48, C:0.19, G:0.22, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1127580 original size:19 final size:19
Alignment explanation
Indices: 1127556--1127617 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
1127546 GCAACGAGAG
1127556 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
1127575 AATCGCAA--C--TA-GAG
1 AATCGCAACGCGAAATGAA
1127589 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
1127608 AATCGCAACG
1 AATCGCAACG
1127618 AGAGAATCAC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 20 0.59
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1127683 original size:14 final size:14
Alignment explanation
Indices: 1127664--1127720 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1127654 TTTGGTTTCG
1127664 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1127678 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1127697 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1127711 CGTTGCGATT
1 CGTTGCGATT
1127721 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1127696 original size:33 final size:33
Alignment explanation
Indices: 1127648--1127728 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1127638 GAAATCACAA
**
1127648 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1127681 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1127714 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
1127729 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1127731 original size:21 final size:21
Alignment explanation
Indices: 1127705--1127780 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1127695 CGCGTTGCGA
1127705 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1127726 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1127746 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1127767 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1127781 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1127761 original size:41 final size:41
Alignment explanation
Indices: 1127704--1127781 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1127694 TCGCGTTGCG
*
1127704 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
1127745 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1127782 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:1127902 original size:33 final size:33
Alignment explanation
Indices: 1127860--1127930 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1127850 AATACTAACT
*
1127860 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1127893 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1127926 TGAAA
1 TGAAA
1127931 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1128162 original size:22 final size:22
Alignment explanation
Indices: 1128110--1128164 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1128100 TGGTTGTGAG
**
1128110 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1128132 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1128154 GGATTTCTTCG
1 GGATTTCTTCG
1128165 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1128333 original size:20 final size:20
Alignment explanation
Indices: 1128308--1128461 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
1128298 CTTTAAATAT
1128308 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1128328 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1128350 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1128369 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
1128389 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1128409 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1128429 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1128449 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1128462 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1128435 original size:40 final size:40
Alignment explanation
Indices: 1128307--1128461 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
1128297 GCTTTAAATA
*
1128307 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
1128348 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
1128388 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
1128428 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
1128462 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:1128478 original size:21 final size:21
Alignment explanation
Indices: 1128448--1128530 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1128438 ATTTTCATAT
*
1128448 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1128469 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1128490 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1128511 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1128531 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1128521 original size:42 final size:43
Alignment explanation
Indices: 1128428--1128526 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1128418 ATTTATGTGT
* *
1128428 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1128469 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1128511 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1128527 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1129033 original size:21 final size:22
Alignment explanation
Indices: 1129010--1129112 Score: 106
Period size: 21 Copynumber: 4.9 Consensus size: 22
1129000 TCGCCTATGT
* *
1129010 CATCTCCAGGATACAGTCCAT-
1 CATCTCCTGGTTACAGTCCATA
* *
1129031 CATCACCTGGCTACAGTCC-TA
1 CATCTCCTGGTTACAGTCCATA
*
1129052 CCTCTCCTGGTTACAGT-CATA
1 CATCTCCTGGTTACAGTCCATA
1129073 CATCTCCTGGTTACAGTCC-TA
1 CATCTCCTGGTTACAGTCCATA
* * *
1129094 CATCACCTGGATATAGTCC
1 CATCTCCTGGTTACAGTCC
1129113 CACGTCACCT
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
20 2 0.03
21 66 0.96
22 1 0.01
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.28
Consensus pattern (22 bp):
CATCTCCTGGTTACAGTCCATA
Found at i:1129082 original size:42 final size:42
Alignment explanation
Indices: 1129010--1129112 Score: 127
Period size: 42 Copynumber: 2.5 Consensus size: 42
1129000 TCGCCTATGT
*
1129010 CATCTCCAGGATACAGTCCATCATCACCTGGCTACAGTCCTA
1 CATCTCCTGGATACAGTCCATCATCACCTGGCTACAGTCCTA
* * * *
1129052 CCTCTCCTGGTTACAGT-CATACATCTCCTGGTTACAGTCCTA
1 CATCTCCTGGATACAGTCCAT-CATCACCTGGCTACAGTCCTA
* *
1129094 CATCACCTGGATATAGTCC
1 CATCTCCTGGATACAGTCC
1129113 CACGTCACCT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
41 3 0.06
42 46 0.92
43 1 0.02
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.28
Consensus pattern (42 bp):
CATCTCCTGGATACAGTCCATCATCACCTGGCTACAGTCCTA
Found at i:1129129 original size:63 final size:63
Alignment explanation
Indices: 1129010--1129154 Score: 152
Period size: 63 Copynumber: 2.3 Consensus size: 63
1129000 TCGCCTATGT
* * * **
1129010 CATCTCCAGGATACAGTCCATCATCACCTGGCTACAGTCCTACCTCTCCTGGTTACAGTCATA
1 CATCTCCAGGATACAGTCCATCATCACCTGGATACAGTCCCACCTCACCTACTTACAGTCATA
* * * * *
1129073 CATCTCCTGGTTACAGTCC-TACATCACCTGGATATAGTCCCACGTCACCTACTTACAGTCCTA
1 CATCTCCAGGATACAGTCCAT-CATCACCTGGATACAGTCCCACCTCACCTACTTACAGTCATA
1129136 GC-T-TACCAGGATACAGTCC
1 -CATCT-CCAGGATACAGTCC
1129155 GACAAGTCCA
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
62 2 0.03
63 64 0.96
64 1 0.01
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.27
Consensus pattern (63 bp):
CATCTCCAGGATACAGTCCATCATCACCTGGATACAGTCCCACCTCACCTACTTACAGTCATA
Found at i:1129258 original size:21 final size:20
Alignment explanation
Indices: 1129234--1129412 Score: 97
Period size: 21 Copynumber: 8.6 Consensus size: 20
1129224 CCCGAGCTAC
1129234 AGCCCAACTTCACCTGCATAT
1 AGCCCAACTTCACCT-CATAT
*
1129255 AGCCCAACTTCACCTGCGTAT
1 AGCCCAACTTCACCT-CATAT
* * * *
1129276 AGCCCCAGTTCTCCATCATAC
1 AGCCCAACTTCACC-TCATAT
* *
1129297 AGCCCAACATCACCATCATAG
1 AGCCCAACTTCACC-TCATAT
* * * *
1129318 AGCCCAACATCTCCTTCGTAC
1 AGCCCAACTTCACC-TCATAT
* *
1129339 AGCCCAACCTCACCCTCCTAT
1 AGCCCAACTTCA-CCTCATAT
* * * * *
1129360 AGCCCCACATCTCCATCGTAA
1 AGCCCAACTTCACC-TCATAT
* *
1129381 AGCCCTACTTCACCTGCTTAT
1 AGCCCAACTTCACCT-CATAT
*
1129402 AGCCCGACTTC
1 AGCCCAACTTC
1129413 TACTGGGTAA
Statistics
Matches: 124, Mismatches: 30, Indels: 8
0.77 0.19 0.05
Matches are distributed among these distances:
20 3 0.02
21 118 0.95
22 3 0.02
ACGTcount: A:0.26, C:0.42, G:0.10, T:0.22
Consensus pattern (20 bp):
AGCCCAACTTCACCTCATAT
Found at i:1129280 original size:42 final size:41
Alignment explanation
Indices: 1129234--1129413 Score: 137
Period size: 42 Copynumber: 4.3 Consensus size: 41
1129224 CCCGAGCTAC
* * *
1129234 AGCCCAACTTCACC-TGCATATAGCCCAACTTCACCTGCGTAT
1 AGCCCAACTTCTCCAT-CATACAGCCCAACTTCACCT-CATAT
* * * *
1129276 AGCCCCAGTTCTCCATCATACAGCCCAACATCACCATCATAG
1 AGCCCAACTTCTCCATCATACAGCCCAACTTCACC-TCATAT
* * * * *
1129318 AGCCCAACATCTCCTTCGTACAGCCCAACCTCACCCTCCTAT
1 AGCCCAACTTCTCCATCATACAGCCCAACTTCA-CCTCATAT
* * * * * *
1129360 AGCCCCACATCTCCATCGTAAAGCCCTACTTCACCTGCTTAT
1 AGCCCAACTTCTCCATCATACAGCCCAACTTCACCT-CATAT
*
1129402 AGCCCGACTTCT
1 AGCCCAACTTCT
1129414 ACTGGGTAAA
Statistics
Matches: 111, Mismatches: 23, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
41 3 0.03
42 104 0.94
43 4 0.04
ACGTcount: A:0.26, C:0.42, G:0.10, T:0.23
Consensus pattern (41 bp):
AGCCCAACTTCTCCATCATACAGCCCAACTTCACCTCATAT
Found at i:1132364 original size:23 final size:23
Alignment explanation
Indices: 1132324--1132412 Score: 87
Period size: 23 Copynumber: 4.0 Consensus size: 23
1132314 TTCGGGACAA
*
1132324 TTATGTGGCACTGT-GGTGCAAAC
1 TTATGTGGTACT-TCGGTGCAAAC
*
1132347 TTATTTGGTACTTCGGTGCAAAC
1 TTATGTGGTACTTCGGTGCAAAC
* *
1132370 ATATGTGGTCCTTCGG-G-ACAA-
1 TTATGTGGTACTTCGGTGCA-AAC
*
1132391 TTATGTGGCACTTCGGTGCAAA
1 TTATGTGGTACTTCGGTGCAAA
1132413 TTACGAGTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
21 14 0.26
22 7 0.13
23 33 0.61
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (23 bp):
TTATGTGGTACTTCGGTGCAAAC
Found at i:1135187 original size:3 final size:3
Alignment explanation
Indices: 1135179--1135211 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1135169 ATATTATCAC
1135179 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1135212 CCAAACAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1137282 original size:40 final size:40
Alignment explanation
Indices: 1137227--1137338 Score: 131
Period size: 40 Copynumber: 2.8 Consensus size: 40
1137217 AAATGATCAA
*
1137227 CAAATTCGCAACGCGAATATGTAAA-TCGCAACACATAAGT
1 CAAATTCGCAACGCG-ATATGTAAATTCGCAACACAAAAGT
* * *
1137267 CAAATTCGCAACGCGATAAT-CAAATTCACAATACAAAAGT
1 CAAATTCGCAACGCGAT-ATGTAAATTCGCAACACAAAAGT
*
1137307 TAAATTCGCAACGCGATA-GTCAAATTCGCAAC
1 CAAATTCGCAACGCGATATGT-AAATTCGCAAC
1137339 GTAAATAGTA
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
39 6 0.10
40 54 0.90
ACGTcount: A:0.43, C:0.23, G:0.13, T:0.21
Consensus pattern (40 bp):
CAAATTCGCAACGCGATATGTAAATTCGCAACACAAAAGT
Found at i:1137339 original size:20 final size:20
Alignment explanation
Indices: 1137227--1137339 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
1137217 AAATGATCAA
1137227 CAAATTCGCAACGCGAATATGT
1 CAAATTCGCAACGCG-ATA-GT
*
1137249 -AAA-TCGCAACAC-ATAAGT
1 CAAATTCGCAACGCGAT-AGT
*
1137267 CAAATTCGCAACGCGATAAT
1 CAAATTCGCAACGCGATAGT
* ** * *
1137287 CAAATTCACAATACAAAAGT
1 CAAATTCGCAACGCGATAGT
*
1137307 TAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
1137327 CAAATTCGCAACG
1 CAAATTCGCAACG
1137340 TAAATAGTAA
Statistics
Matches: 71, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
18 4 0.06
19 4 0.06
20 58 0.82
21 5 0.07
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGATAGT
Found at i:1137374 original size:20 final size:20
Alignment explanation
Indices: 1137307--1137398 Score: 114
Period size: 20 Copynumber: 4.5 Consensus size: 20
1137297 ATACAAAAGT
* *
1137307 TAAATTCGCAACGCG-ATAG
1 TAAAATCGCAACGTGAATAG
* *
1137326 TCAAATTCGCAACGTAAATAG
1 T-AAAATCGCAACGTGAATAG
1137347 TAAAAATCGCAACGTGAATAG
1 T-AAAATCGCAACGTGAATAG
*
1137368 TAAAATCACAACGTGAATAG
1 TAAAATCGCAACGTGAATAG
1137388 TAAAATCGCAA
1 TAAAATCGCAA
1137399 TGAATCTATA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
19 1 0.02
20 40 0.62
21 23 0.36
ACGTcount: A:0.46, C:0.17, G:0.16, T:0.21
Consensus pattern (20 bp):
TAAAATCGCAACGTGAATAG
Found at i:1137380 original size:41 final size:40
Alignment explanation
Indices: 1137272--1137398 Score: 125
Period size: 40 Copynumber: 3.1 Consensus size: 40
1137262 TAAGTCAAAT
* * * *
1137272 TCGCAACGCGATAATCAAATTCACAA--TACAAAAGTTAAAT
1 TCGCAACGCGATAGTCAAAATCACAACGTA-AATAG-TAAAA
* *
1137312 TCGCAACGCGATAGTCAAATTCGCAACGTAAATAGTAAAAA
1 TCGCAACGCGATAGTCAAAATCACAACGTAAATAGT-AAAA
* *
1137353 TCGCAACGTGAATAGT-AAAATCACAACGTGAATAGTAAAA
1 TCGCAACGCG-ATAGTCAAAATCACAACGTAAATAGTAAAA
1137393 TCGCAA
1 TCGCAA
1137399 TGAATCTATA
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
40 35 0.47
41 33 0.44
42 7 0.09
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.20
Consensus pattern (40 bp):
TCGCAACGCGATAGTCAAAATCACAACGTAAATAGTAAAA
Found at i:1137791 original size:20 final size:20
Alignment explanation
Indices: 1137749--1137799 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1137739 CAACGCGATT
*
1137749 TTGCGATTTTCTAAATTCGCG
1 TTGCGATTTTCT-AATTCACG
1137770 TTGCGATTTTACT-ATTCACG
1 TTGCGATTTT-CTAATTCACG
*
1137790 TTGCGCTTTT
1 TTGCGATTTT
1137800 GGAAACTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 15 0.56
21 10 0.37
22 2 0.07
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.47
Consensus pattern (20 bp):
TTGCGATTTTCTAATTCACG
Found at i:1137847 original size:19 final size:19
Alignment explanation
Indices: 1137809--1137856 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1137799 TGGAAACTGA
* *
1137809 GTTGCGAAATTGGAGTTCGC
1 GTTGCG-AATTCGAGATCGC
1137829 GTTGCGAATTCGAGATCGC
1 GTTGCGAATTCGAGATCGC
1137848 GTTGC-AATT
1 GTTGCGAATT
1137857 TTGTTGGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 4 0.15
19 16 0.62
20 6 0.23
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (19 bp):
GTTGCGAATTCGAGATCGC
Found at i:1139018 original size:29 final size:30
Alignment explanation
Indices: 1138942--1139019 Score: 72
Period size: 29 Copynumber: 2.6 Consensus size: 30
1138932 TAAATTACAA
*
1138942 AATTT-CTCACTCAACTTTTCTCTTTCTCC
1 AATTTACTCACTAAACTTTTCTCTTTCTCC
* * **
1138971 TATTTCACTCATTGTACTTTTAC-CTTT-TCC
1 AATTT-ACTCACTAAACTTTT-CTCTTTCTCC
1139001 AATTTACTCACTAAACTTT
1 AATTTACTCACTAAACTTT
1139020 CAAAATGCTC
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
29 15 0.39
30 7 0.18
31 15 0.39
32 1 0.03
ACGTcount: A:0.22, C:0.28, G:0.01, T:0.49
Consensus pattern (30 bp):
AATTTACTCACTAAACTTTTCTCTTTCTCC
Found at i:1140571 original size:26 final size:23
Alignment explanation
Indices: 1140495--1140551 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
1140485 TATCATAAGC
1140495 ATTATCGATTTCAAATTAATGAT
1 ATTATCGATTTCAAATTAATGAT
1140518 ATTATCGATTTCAAATTAATGAT
1 ATTATCGATTTCAAATTAATGAT
1140541 ATTATCGATTT
1 ATTATCGATTT
1140552 AAACCTAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (23 bp):
ATTATCGATTTCAAATTAATGAT
Found at i:1142113 original size:16 final size:17
Alignment explanation
Indices: 1142078--1142114 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1142068 TTATGGGATG
1142078 AAAAATAGTATTATTGT
1 AAAAATAGTATTATTGT
1142095 AAAAAT-GTAATTATT-T
1 AAAAATAGT-ATTATTGT
1142111 AAAA
1 AAAA
1142115 TAATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (17 bp):
AAAAATAGTATTATTGT
Found at i:1142155 original size:17 final size:17
Alignment explanation
Indices: 1142133--1142165 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1142123 TACTATCATA
*
1142133 ATATTATTTTTTATATT
1 ATATTATATTTTATATT
1142150 ATATTATATTTTATAT
1 ATATTATATTTTATAT
1142166 AAATAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:1149425 original size:27 final size:27
Alignment explanation
Indices: 1149392--1149452 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
1149382 CACAACGTGC
* *
1149392 TATATATACATTATATAATATAAACAA
1 TATATATACAATATACAATATAAACAA
* * *
1149419 TATATATATAATATACATTATAAATAA
1 TATATATACAATATACAATATAAACAA
1149446 -ATATATA
1 TATATATA
1149453 GTCAAATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (27 bp):
TATATATACAATATACAATATAAACAA
Found at i:1150224 original size:32 final size:35
Alignment explanation
Indices: 1150188--1150267 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 35
1150178 ATTATTCTTC
*
1150188 GTGAAGTTGAAATCTTTG-A-TGG-CTCATTCGTT
1 GTGAAGTTGAAATCTTTGAATTGGAATCATTCGTT
*
1150220 GTGAAGTTG-AA-CTTTGAATTGGATATCTTTCGTT
1 GTGAAGTTGAAATCTTTGAATTGGA-ATCATTCGTT
1150254 GTGAAGTTGAAATC
1 GTGAAGTTGAAATC
1150268 ACATCTTGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 5 0.12
31 3 0.08
32 12 0.30
34 17 0.43
35 2 0.05
36 1 0.03
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (35 bp):
GTGAAGTTGAAATCTTTGAATTGGAATCATTCGTT
Found at i:1151219 original size:56 final size:55
Alignment explanation
Indices: 1151122--1151228 Score: 135
Period size: 56 Copynumber: 1.9 Consensus size: 55
1151112 TTTCTTTTTC
* * * *
1151122 TTTTTCTTTCCTTTTTTCGATTTAGGGCGTCCTTTCGGGTTTTCACCCTAAATGT
1 TTTTTCTTTCCTTTTTTCGACTTAGGACGTCCTCTCAGGTTTTCACCCTAAATGT
* *
1151177 TTTTTCTTTTCTTTTTTTCGACTTAGGACG-CTCTCTCAGGTTTTCATCCTAA
1 TTTTTC-TTTCCTTTTTTCGACTTAGGACGTC-CTCTCAGGTTTTCACCCTAA
1151229 GTGAAGTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
55 7 0.16
56 37 0.84
ACGTcount: A:0.12, C:0.22, G:0.14, T:0.51
Consensus pattern (55 bp):
TTTTTCTTTCCTTTTTTCGACTTAGGACGTCCTCTCAGGTTTTCACCCTAAATGT
Found at i:1161163 original size:13 final size:13
Alignment explanation
Indices: 1161145--1161173 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1161135 AAATTTAAAT
1161145 TTACCCTTTTCAC
1 TTACCCTTTTCAC
1161158 TTACCCTTTTCAC
1 TTACCCTTTTCAC
1161171 TTA
1 TTA
1161174 AGAAGACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.48
Consensus pattern (13 bp):
TTACCCTTTTCAC
Found at i:1161732 original size:3 final size:3
Alignment explanation
Indices: 1161721--1161757 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1161711 AAAAAGAAGG
1161721 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1161758 AACAGAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1161921 original size:2 final size:2
Alignment explanation
Indices: 1161916--1161942 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1161906 AAAATAAGAA
1161916 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1161943 ATGTAGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1164789 original size:22 final size:22
Alignment explanation
Indices: 1164764--1164836 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 22
1164754 TATATTATAT
1164764 AAATCAAAGAAAAAATTAAAAA
1 AAATCAAAGAAAAAATTAAAAA
* *
1164786 AAATCAAA-AATAAATAAAAAA
1 AAATCAAAGAAAAAATTAAAAA
*
1164807 TAAATCAAAGGGAAAAAAGTAAATAA
1 -AAATCAAA--GAAAAAATTAAA-AA
1164833 AAAT
1 AAAT
1164837 GTTAAATAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
21 11 0.27
22 16 0.39
25 12 0.29
26 2 0.05
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (22 bp):
AAATCAAAGAAAAAATTAAAAA
Found at i:1164795 original size:11 final size:11
Alignment explanation
Indices: 1164764--1164815 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
1164754 TATATTATAT
1164764 AAATCAAAGAAA
1 AAATCAAA-AAA
*
1164776 AAAT-TAAAAA
1 AAATCAAAAAA
*
1164786 AAATCAAAAAT
1 AAATCAAAAAA
1164797 AAAT-AAAAAA
1 AAATCAAAAAA
1164807 TAAATCAAA
1 -AAATCAAA
1164816 GGGAAAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 12 0.36
11 14 0.42
12 7 0.21
ACGTcount: A:0.77, C:0.06, G:0.02, T:0.15
Consensus pattern (11 bp):
AAATCAAAAAA
Found at i:1164875 original size:21 final size:21
Alignment explanation
Indices: 1164840--1164909 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
1164830 TAAAAATGTT
*
1164840 AAATAAAGTAATAAAATAAA-A
1 AAATAAA-TAGTAAAATAAATA
1164861 ATAATAAGA-AGTAAAA-AAATAA
1 A-AATAA-ATAGTAAAATAAAT-A
1164883 AAATAAATAG-AAAATAAATA
1 AAATAAATAGTAAAATAAATA
1164903 AAATAAA
1 AAATAAA
1164910 AACCGCTATA
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
20 16 0.38
21 18 0.43
22 7 0.17
23 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.19
Consensus pattern (21 bp):
AAATAAATAGTAAAATAAATA
Found at i:1164879 original size:24 final size:25
Alignment explanation
Indices: 1164844--1164911 Score: 86
Period size: 24 Copynumber: 2.7 Consensus size: 25
1164834 AATGTTAAAT
*
1164844 AAAGTAATAAAATAAAAAT-AATA-
1 AAAGTAAAAAAATAAAAATAAATAG
1164867 AGAAGTAAAAAAATAAAAATAAATAG
1 A-AAGTAAAAAAATAAAAATAAATAG
*
1164893 AAAATAAATAAAATAAAAA
1 AAAGTAAA-AAAATAAAAA
1164912 CCGCTATAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 1 0.03
24 17 0.44
25 10 0.26
26 11 0.28
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (25 bp):
AAAGTAAAAAAATAAAAATAAATAG
Found at i:1164898 original size:11 final size:10
Alignment explanation
Indices: 1164780--1164909 Score: 59
Period size: 11 Copynumber: 12.0 Consensus size: 10
1164770 AAGAAAAAAT
1164780 TAAAAA-AAA
1 TAAAAATAAA
1164789 TCAAAAATAAA
1 T-AAAAATAAA
1164800 TAAAAAATAAA
1 T-AAAAATAAA
* ***
1164811 TCAAAGGGAA
1 TAAAAATAAA
*
1164821 -AAAAGTAAA
1 TAAAAATAAA
1164830 TAAAAATGTTAAA
1 TAAAAA---TAAA
1164843 TAAAGTAATAAAA
1 TAAA--AAT-AAA
1164856 TAAAAATAATAA
1 TAAAAAT-A-AA
* *
1164868 GAAGTAAAAAAA
1 TAA--AAATAAA
1164880 TAAAAATAAA
1 TAAAAATAAA
1164890 TAGAAAATAAA
1 TA-AAAATAAA
1164901 T-AAAATAAA
1 TAAAAATAAA
1164910 AACCGCTATA
Statistics
Matches: 95, Mismatches: 13, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
9 15 0.16
10 22 0.23
11 28 0.29
12 9 0.09
13 16 0.17
14 3 0.03
15 2 0.02
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:1164942 original size:25 final size:23
Alignment explanation
Indices: 1164914--1164974 Score: 70
Period size: 25 Copynumber: 2.6 Consensus size: 23
1164904 AATAAAAACC
1164914 GCTATAACTAAAAAGGAAAAAGAAT
1 GCTATAACTAAAAAGG-AAAA-AAT
* *
1164939 GCTAAAATTAAAAAGGAAAAAAT
1 GCTATAACTAAAAAGGAAAAAAT
*
1164962 G-AATAACTAAAAA
1 GCTATAACTAAAAA
1164975 TTTAAAGGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 9 0.29
23 4 0.13
24 4 0.13
25 14 0.45
ACGTcount: A:0.64, C:0.07, G:0.13, T:0.16
Consensus pattern (23 bp):
GCTATAACTAAAAAGGAAAAAAT
Found at i:1165373 original size:19 final size:19
Alignment explanation
Indices: 1165339--1165375 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1165329 ATGACCAACA
* *
1165339 AAATCGCAATGTGATCTCT
1 AAATCGCAACGCGATCTCT
1165358 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1165376 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1165466 original size:21 final size:21
Alignment explanation
Indices: 1165420--1165473 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
1165410 GATTTTGACT
*
1165420 ATCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTACAAA
* * *
1165441 TTCGCGTTGCGATTTTAGAAA
1 ATCGCATTGCGATTTTACAAA
*
1165462 ATCGCAATGCGA
1 ATCGCATTGCGA
1165474 ATATGTAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (21 bp):
ATCGCATTGCGATTTTACAAA
Found at i:1165505 original size:20 final size:20
Alignment explanation
Indices: 1165482--1165535 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1165472 GAATATGTAA
1165482 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
1165502 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1165522 ATCGCAATGCGATT
1 ATCGCAACGCGATT
1165536 TTCAAAGCGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1166170 original size:20 final size:20
Alignment explanation
Indices: 1166133--1166170 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1166123 TCAAATTCAC
* *
1166133 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTAAGTTTCGT
1166153 GTTGCGATTTTAAGTTTC
1 GTTGCGATTTTAAGTTTC
1166171 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.53
Consensus pattern (20 bp):
GTTGCGATTTTAAGTTTCGT
Found at i:1168100 original size:20 final size:20
Alignment explanation
Indices: 1168077--1168144 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
1168067 GAAACTTAAA
1168077 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1168097 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
1168117 ATCGCAAAGC-AAATTTGACT
1 ATCGCAACGCGAAA-ATGACT
1168137 ATCGCAAC
1 ATCGCAAC
1168145 TGTAACACCC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 2 0.05
20 40 0.95
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1168847 original size:23 final size:23
Alignment explanation
Indices: 1168821--1168867 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1168811 GTCACCACAG
*
1168821 CTCGTATAATTGCACCGAAGTGC
1 CTCGTAGAATTGCACCGAAGTGC
*
1168844 CTCGTAGAATTGCACCGTAGTGC
1 CTCGTAGAATTGCACCGAAGTGC
1168867 C
1 C
1168868 ATATAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (23 bp):
CTCGTAGAATTGCACCGAAGTGC
Found at i:1170489 original size:21 final size:21
Alignment explanation
Indices: 1170465--1170509 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1170455 TTTTGTTCGT
* *
1170465 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1170486 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1170507 TTG
1 TTG
1170510 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1173821 original size:23 final size:23
Alignment explanation
Indices: 1173795--1173839 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1173785 CACCACAGCT
*
1173795 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
1173818 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
1173840 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:1175461 original size:21 final size:21
Alignment explanation
Indices: 1175437--1175481 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1175427 TTTTGTTCGT
* *
1175437 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1175458 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1175479 TTG
1 TTG
1175482 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1176232 original size:33 final size:34
Alignment explanation
Indices: 1176185--1176257 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 34
1176175 GGATGTTACA
*
1176185 GCAACGGGATAATCGCAATGCG-AAATAAAAATC
1 GCAACGGGAAAATCGCAATGCGAAAATAAAAATC
* *
1176218 GCAACGTGAAAATCGCAATGCGAAAATGAAAATC
1 GCAACGGGAAAATCGCAATGCGAAAATAAAAATC
1176252 GCAACG
1 GCAACG
1176258 CGAATTTAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 20 0.56
34 16 0.44
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (34 bp):
GCAACGGGAAAATCGCAATGCGAAAATAAAAATC
Found at i:1176247 original size:20 final size:20
Alignment explanation
Indices: 1176224--1176261 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1176214 AATCGCAACG
*
1176224 TGAAAATCGCAATGCGAAAA
1 TGAAAATCGCAACGCGAAAA
1176244 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
1176262 TTTAGTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACGCGAAAA
Found at i:1176310 original size:20 final size:20
Alignment explanation
Indices: 1176287--1176330 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1176277 CGATAGTCAT
1176287 TTTCGCATTGCGATTTTAAG
1 TTTCGCATTGCGATTTTAAG
**
1176307 TTTCGTGTTGCGATTTTAAG
1 TTTCGCATTGCGATTTTAAG
1176327 TTTC
1 TTTC
1176331 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCATTGCGATTTTAAG
Found at i:1176901 original size:21 final size:21
Alignment explanation
Indices: 1176806--1176913 Score: 110
Period size: 21 Copynumber: 5.1 Consensus size: 21
1176796 GCCCGACTCA
1176806 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
1176827 TCT-CCTATCGTTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* ** *
1176848 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
* *
1176869 CCTCTCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
1176890 CCTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
1176911 CCT
1 CCT
1176914 CCCACCATTC
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
20 1 0.01
21 67 0.97
22 1 0.01
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.25
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:1176907 original size:42 final size:41
Alignment explanation
Indices: 1176806--1176928 Score: 131
Period size: 42 Copynumber: 2.9 Consensus size: 41
1176796 GCCCGACTCA
* * *
1176806 CCTGTCATCGTTCAAGAGGCCTCTCCTATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCC-ACCGTTCAAGAGGCC
* **
1176848 CCTATCATCCCTCAAGAGTCCCCTCTCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTC-CACCGTTCAAGAGGCC
* *
1176890 CCTGTCATCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTGTCATCGTTCAAGA-GTCCCCT-CCACCGTTCAAGAG
1176929 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
42 63 0.94
43 4 0.06
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.24
Consensus pattern (41 bp):
CCTGTCATCGTTCAAGAGTCCCCTCCACCGTTCAAGAGGCC
Found at i:1176927 original size:21 final size:21
Alignment explanation
Indices: 1176814--1176928 Score: 76
Period size: 21 Copynumber: 5.5 Consensus size: 21
1176804 CACCTGTCAT
*
1176814 CGTTCAAGAGG--CCTCTCCTAT
1 CGTTCAAGAGGTCCCTCT-C-AC
* *
1176835 CGTTCAAGAGGCCCCTATCATC
1 CGTTCAAGAGGTCCCTCTCA-C
*
1176857 C-CTCAAGA-GTCCCCTCTCAC
1 CGTTCAAGAGGT-CCCTCTCAC
* * *
1176877 CGTTCAAGAGGCCCCTGTCAT
1 CGTTCAAGAGGTCCCTCTCAC
* *
1176898 CGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGTCCCTCTCAC
*
1176919 CATTCAAGAG
1 CGTTCAAGAG
1176929 CCCGATTCAC
Statistics
Matches: 72, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
20 3 0.04
21 62 0.86
22 3 0.04
23 4 0.06
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
CGTTCAAGAGGTCCCTCTCAC
Found at i:1178333 original size:14 final size:14
Alignment explanation
Indices: 1178314--1178348 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1178304 GCTTGTTTAA
1178314 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
1178328 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
1178342 TTGATTT
1 TTGATTT
1178349 AATTGATGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1178505 original size:20 final size:20
Alignment explanation
Indices: 1178480--1178543 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
1178470 AACACTAAAC
*
1178480 TCAAAATCACAATGCGAAAG
1 TCAAAATCGCAATGCGAAAG
1178500 TCAAAATCGCAATGCGAAAG
1 TCAAAATCGCAATGCGAAAG
* *
1178520 CCAAAATCGCAACGCGAAAG
1 TCAAAATCGCAATGCGAAAG
1178540 TCAA
1 TCAA
1178544 TTCGCATTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.12
Consensus pattern (20 bp):
TCAAAATCGCAATGCGAAAG
Found at i:1178611 original size:20 final size:20
Alignment explanation
Indices: 1178582--1178718 Score: 184
Period size: 20 Copynumber: 6.8 Consensus size: 20
1178572 ACGATTTTCT
*
1178582 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
1178602 CGTTGTGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1178622 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
* *
1178642 CATTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1178662 CATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1178682 CATTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
*
1178702 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
1178719 GAATGTGTAA
Statistics
Matches: 104, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 104 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1178912 original size:18 final size:18
Alignment explanation
Indices: 1178889--1178923 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1178879 AAGCCGGTTG
*
1178889 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1178907 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1178924 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1181251 original size:24 final size:24
Alignment explanation
Indices: 1181200--1181251 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1181190 ATCCAAGTAT
** *
1181200 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
1181224 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
1181248 TGAC
1 TGAC
1181252 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:1182083 original size:20 final size:20
Alignment explanation
Indices: 1182058--1182227 Score: 132
Period size: 20 Copynumber: 8.4 Consensus size: 20
1182048 GAAATTCAGT
*
1182058 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
1182078 GTTGCGATAGTCAGAATCGA
1 GTTGCGATAGTCAGAATCGC
* **
1182098 GTTGCAATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
1182119 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* ** *
1182139 GTTACGATTATGT-ATTATTGC
1 GTTGCGA-TA-GTCAGAATCGC
* *
1182160 GTTACGATAGTCAGAATC-T
1 GTTGCGATAGTCAGAATCGC
** *
1182179 GTTGCGATTATGT-ATTATCGT
1 GTTGCGA-TA-GTCAGAATCGC
1182200 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
1182220 GTTGCGAT
1 GTTGCGAT
1182228 TTACATATTT
Statistics
Matches: 117, Mismatches: 23, Indels: 20
0.73 0.14 0.12
Matches are distributed among these distances:
19 12 0.10
20 64 0.55
21 37 0.32
22 4 0.03
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:1182118 original size:41 final size:41
Alignment explanation
Indices: 1182073--1182228 Score: 242
Period size: 41 Copynumber: 3.8 Consensus size: 41
1182063 GACAGTCAGA
* *
1182073 ATCGCGTTGCGATAGTCAGAATCGAGTTGCAATTATGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
*
1182114 ATCGCGTTGCGATAGTCAGAATCGCGTTACGATTATGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
* * *
1182155 ATTGCGTTACGATAGTCAGAATC-TGTTGCGATTATGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
*
1182195 ATCGTGTTGCGATAGTCAGAATCGCGTTGCGATT
1 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATT
1182229 TACATATTTG
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 35 0.34
41 68 0.66
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
Found at i:1182212 original size:81 final size:82
Alignment explanation
Indices: 1182076--1182228 Score: 254
Period size: 81 Copynumber: 1.9 Consensus size: 82
1182066 AGTCAGAATC
*
1182076 GCGTTGCGATAGTCAGAATCGAGTTGCAATTATGTATTATCGCGTTGCGATAGTCAGAATCGCGT
1 GCGTTACGATAGTCAGAATCGAGTTGCAATTATGTATTATCGCGTTGCGATAGTCAGAATCGCGT
1182141 TACGATTATGTATTATT
66 TACGATTATGTATTATT
* * *
1182158 GCGTTACGATAGTCAGAATC-TGTTGCGATTATGTATTATCGTGTTGCGATAGTCAGAATCGCGT
1 GCGTTACGATAGTCAGAATCGAGTTGCAATTATGTATTATCGCGTTGCGATAGTCAGAATCGCGT
*
1182222 TGCGATT
66 TACGATT
1182229 TACATATTTG
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
81 47 0.71
82 19 0.29
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.35
Consensus pattern (82 bp):
GCGTTACGATAGTCAGAATCGAGTTGCAATTATGTATTATCGCGTTGCGATAGTCAGAATCGCGT
TACGATTATGTATTATT
Found at i:1183963 original size:84 final size:84
Alignment explanation
Indices: 1183725--1184947 Score: 1449
Period size: 84 Copynumber: 14.6 Consensus size: 84
1183715 AATGGAATCA
* * * **
1183725 AACTCGAAGGT-TTTTGTTGGTAGATAGCCCTTCTCGCCTTGAGCTAAACTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCC
* * * *
1183789 TTAGAGCTGAGTGTAATCA
66 TTGGAGCTGAGCGTAGTCG
* * * * *
1183808 AACTCGAATGTC--TTGCTTGACAGATAACCCTTCTCA-CATTGAGTTATGCTGTAAATGATGTG
1 AACTCGAAGGTCTTTTG-TTGGCAGATAACCCTTCT-AGCCTTGAGCTATGCTGCAAATGATGTG
* ** *
1183870 CCTTTGAGCTGAGTATAATCG
64 CCTTGGAGCTGAGCGTAGTCG
* * * *
1183891 AACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATAATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCC
**
1183956 TTGGAGCTGAGCGTAGTTA
66 TTGGAGCTGAGCGTAGTCG
* * * *
1183975 AACTCGAAGGTCTTTTGTTGGTAGATAAGCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTACC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCC
* *
1184040 TTGAAGCTTAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * * *
1184059 AACTCGAAGGTATTTTGTTGGCAAATAACCCTCCTTA-CCTTGAGCTATGTTGCAAATGATGTGC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTC-TAGCCTTGAGCTATGCTGCAAATGATGTGC
*
1184123 CTTGGAGCTGAGCGTAGTCA
65 CTTGGAGCTGAGCGTAGTCG
* * * *
1184143 AACTCGAAGGTGTTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTACAAATGATATGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCC
*
1184208 TTGGAGCTGAGCGTAGTCA
66 TTGGAGCTGAGCGTAGTCG
* * * * * *
1184227 AACTCGAAGGTCTTTTGTTGGCAAAAAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATACC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCC
*
1184292 TTGGAGCTGAACGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * *
1184311 AACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTAGCCATGAGCTATGCTG-TAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCC
* *
1184375 TTAGAGCT-ACGCGTAGTTG
66 TTGGAGCTGA-GCGTAGTCG
* * * *
1184394 AACTCGAAGGTATTTGGTTGGCAGATAACCCTTTTAGCCTTGAGTTATGCTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCC
*
1184459 TTGGAGCTAAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * * * *
1184478 AACCCGAAGGTCTTTTGGTGGCAGATAACCCTTCTAGTCC-TGAGCTATGCTACAAATAATATGC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG-CCTTGAGCTATGCTGCAAATGATGTGC
* *
1184542 CTTAGAGCTGAACGTAGTCG
65 CTTGGAGCTGAGCGTAGTCG
* * * * *
1184562 AACTTGAAGGTCTTTTGGTGGCAAATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCC
* *
1184627 TTGGAGCTAAGCGTAGTCA
66 TTGGAGCTGAGCGTAGTCG
* * *
1184646 AACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTAGCCTTGAGCTATGTTACAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCC
1184711 TTGGAGCTGAGCGTAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * * * *
1184730 AACTCAAAGGTCTTTGGTTGGCAGATAACCATTCTAGCCTTGAGTTATGCTACAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCC
* *
1184795 TTAGAGCTGAGCGAAGTCG
66 TTGGAGCTGAGCGTAGTCG
* * * * * *
1184814 AACTTGAAAGTC-TTTG-GGGACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTGC
1 AACTCGAAGGTCTTTTGTTGG-CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGC
* * * *
1184877 CTTTGAGCTGAGTGTAATCA
65 CTTGGAGCTGAGCGTAGTCG
* * * * * *
1184897 AACTCGAAGGTCTTTGGCTGACAGCTAACCCTTCTCGCCTTGAGTTATGCT
1 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCT
1184948 ACCAATAGTT
Statistics
Matches: 976, Mismatches: 148, Indels: 31
0.85 0.13 0.03
Matches are distributed among these distances:
82 6 0.01
83 215 0.22
84 746 0.76
85 9 0.01
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCC
TTGGAGCTGAGCGTAGTCG
Found at i:1184908 original size:419 final size:416
Alignment explanation
Indices: 1183705--1184954 Score: 1541
Period size: 419 Copynumber: 3.0 Consensus size: 416
1183695 TTTGTCATGC
* * * * *
1183705 CCTT-GAGCTGAATGGAATCAAACTCGAAGGTTTTTGTTGGTAGATAGCCCTTCTCGCCTTGAGC
1 CCTTAGAGCTGAACGTAGTCAAACTCGAAGGTTTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGC
** * * * * * *
1183769 TAAACTGCAAATGATGTGCCTTAGAGCTGAGTGTAATCAAACTCGAATGTC--TTGCTTGACAGA
66 TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTG-TTGGCAGA
* * ** *
1183832 TAACCCTTCTCA-CATTGAGTTATGCTGTAAATGATGTGCCTTTGAGCTGAGTATAATCGAACTC
130 TAACCCTTCT-AGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * * *
1183896 GAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATAATGTGCCTTGGA
194 GAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCT-CAAATGATGTGCCTTAGA
* * * *
1183961 GCTGAGCGTAGTTAAACTCGAAGGTCTTTTGTTGGTAGATAAGCCTTCTAGCCTTGAGTTATGCT
258 GCTGAGCGTAGTTGAACTCGAAGGTC-TTTG-GGGCAGATAACCCTTCTAGCCTTGAGTTATGCT
* * * * *
1184026 GCAAATGATGTACC-TTGAAGCTTAGCGTAGTCGAACTCGAAGGTATTTTGTTGGCAAATAACCC
321 GCAAATGATGTGCCTTTG-AGCTAAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGATAACCC
* * * * *
1184090 TCCT-TACCTTGAGCTATGTTGCAAATGATGTG
385 TTCTGT-CCTTGAGCTATGCTACAAATAATATG
* *
1184122 CCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTGTTTTGTTGGCAGATAGCCCTTCTAGCCTTGAG
1 CCTTAGAGCTGAACGTAGTCAAACTCGAAGGT-TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAG
* *
1184187 CTATGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAAA
65 CTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAGA
* * * *
1184252 AAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATACCTTGGAGCTGAACGTAGTCGAACTCG
130 TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCG
* **
1184317 AAGGTCTTTTGG-TGGCAGATAACCCTTCTAGCCATGAGCTATGCTGTAATGATGTGCCTTAGAG
195 AAGGTC-TTTGGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTCAAATGATGTGCCTTAGAG
* *
1184381 CT-ACGCGTAGTTGAACTCGAAGGTATTTGGTTGGCAGATAACCCTTTTAGCCTTGAGTTATGCT
259 CTGA-GCGTAGTTGAACTCGAAGGTCTTTGG--GGCAGATAACCCTTCTAGCCTTGAGTTATGCT
* *
1184445 GCAAATGATGTGCCTTGGAGCTAAGCGTAGTCGAACCCGAAGGTCTTTTGGTGGCAGATAACCCT
321 GCAAATGATGTGCCTTTGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCT
1184510 TCTAGTCC-TGAGCTATGCTACAAATAATATG
386 TCT-GTCCTTGAGCTATGCTACAAATAATATG
* * * *
1184541 CCTTAGAGCTGAACGTAGTCGAACTTGAAGGTCTTTTGGTGGCAAATAGCCCTTCTAGCCTTGAG
1 CCTTAGAGCTGAACGTAGTCAAACTCGAAGGT-TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAG
* *
1184606 CTATGCTGCAAATGATATGCCTTGGAGCTAAGCGTAGTCAAACTCGAAGGTCTTTTGGTGGCAGA
65 CTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAGA
* * ** *
1184671 TAACCCTTCTAGCCTTGAGCTATGTTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCA
130 TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCG
* *
1184736 AAGGTCTTTGGTTGGCAGATAACCATTCTAGCCTTGAGTTATGCTACAAATGATGTGCCTTAGAG
195 AAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCT-CAAATGATGTGCCTTAGAG
* * * * * *
1184801 CTGAGCGAAGTCGAACTTGAAAGTCTTTGGGGACAGATAACCCTTCTAGCCTTGAGTTATACTGT
259 CTGAGCGTAGTTGAACTCGAAGGTCTTTGGGG-CAGATAACCCTTCTAGCCTTGAGTTATGCTGC
* * * * * *
1184866 AAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTC-TTTGGCTGACAGCTAACCCTT
323 AAATGATGTGCCTTTGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGGCAGATAACCCTT
* *
1184930 CTCG-CCTTGAGTTATGCTACCAATA
387 CT-GTCCTTGAGCTATGCTACAAATA
1184955 GTTTCTTTAA
Statistics
Matches: 719, Mismatches: 96, Indels: 34
0.85 0.11 0.04
Matches are distributed among these distances:
417 4 0.01
418 42 0.06
419 525 0.73
420 139 0.19
421 9 0.01
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (416 bp):
CCTTAGAGCTGAACGTAGTCAAACTCGAAGGTTTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGC
TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAGAT
AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGA
AGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTCAAATGATGTGCCTTAGAGCT
GAGCGTAGTTGAACTCGAAGGTCTTTGGGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA
TGATGTGCCTTTGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTGT
CCTTGAGCTATGCTACAAATAATATG
Found at i:1186252 original size:99 final size:100
Alignment explanation
Indices: 1186124--1186329 Score: 335
Period size: 100 Copynumber: 2.1 Consensus size: 100
1186114 CTCAATATCG
*
1186124 TTGTATAGATATTATAATCACCTTTATCAGGCT-AGCTGAATATTATCCATAAAG-CTGAGGCGT
1 TTGTATAGATATTATAATCACCTTTATCAGGATCAGCTGAATATTATCCATAAAGTC-GAGGCGT
*
1186187 TTAACCAAGTGCTCTAGAGGGATACCTCAAGCTTTA
65 TTAACCAAGTGCTCTAGAGGGATAACTCAAGCTTTA
* *
1186223 TTGTATAGATATTATAATCACCTTTATCAGGATCAGCTGAATCTTATCCATAAAGTCGAGGTGTT
1 TTGTATAGATATTATAATCACCTTTATCAGGATCAGCTGAATATTATCCATAAAGTCGAGGCGTT
* *
1186288 TAACCAATTGCTTTAGAGGGATAACTCAAGCTTTA
66 TAACCAAGTGCTCTAGAGGGATAACTCAAGCTTTA
1186323 TTGTATA
1 TTGTATA
1186330 TATGTAATAT
Statistics
Matches: 99, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
99 32 0.32
100 66 0.67
101 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (100 bp):
TTGTATAGATATTATAATCACCTTTATCAGGATCAGCTGAATATTATCCATAAAGTCGAGGCGTT
TAACCAAGTGCTCTAGAGGGATAACTCAAGCTTTA
Found at i:1188935 original size:12 final size:12
Alignment explanation
Indices: 1188918--1188953 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
1188908 TATATATTAT
1188918 ATAAATCAAAGA
1 ATAAATCAAAGA
*
1188930 ATAAATAAAAAGA
1 ATAAAT-CAAAGA
1188943 ATAAATCAAAG
1 ATAAATCAAAG
1188954 GGAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.69, C:0.06, G:0.08, T:0.17
Consensus pattern (12 bp):
ATAAATCAAAGA
Found at i:1189016 original size:17 final size:15
Alignment explanation
Indices: 1188987--1189050 Score: 58
Period size: 17 Copynumber: 3.9 Consensus size: 15
1188977 TTAAATAAAG
1188987 TAATAAAAT-AAAAA
1 TAATAAAATAAAAAA
1189001 TAATAAGAAGTAAAAAA
1 TAATAA-AA-TAAAAAA
*
1189018 TAAAAATAAATAAATAAA
1 T-AATA-AAATAAA-AAA
1189036 TAAATAAAATAAAAA
1 T-AATAAAATAAAAA
1189051 CCGCTAAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
14 6 0.14
15 2 0.05
16 3 0.07
17 17 0.40
18 13 0.31
19 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (15 bp):
TAATAAAATAAAAAA
Found at i:1189081 original size:25 final size:24
Alignment explanation
Indices: 1189053--1189114 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
1189043 AATAAAAACC
*
1189053 GCTAAAACTAAAAAGGAAAAAGAAT
1 GCTAAAACTAAAAAAGAAAAA-AAT
*
1189078 GCTAAAATTAAAAAAGAAAAAAAT
1 GCTAAAACTAAAAAAGAAAAAAAT
1189102 G--AATAACTAAAAA
1 GCTAA-AACTAAAAA
1189115 TTTAAAGGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 2 0.06
23 8 0.24
24 4 0.12
25 19 0.58
ACGTcount: A:0.68, C:0.06, G:0.11, T:0.15
Consensus pattern (24 bp):
GCTAAAACTAAAAAAGAAAAAAAT
Found at i:1190558 original size:14 final size:14
Alignment explanation
Indices: 1190539--1190565 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1190529 AAAAATTTTA
1190539 AGTTATTTGAGTCG
1 AGTTATTTGAGTCG
1190553 AGTTATTTGAGTC
1 AGTTATTTGAGTC
1190566 AAATTGAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.26, T:0.44
Consensus pattern (14 bp):
AGTTATTTGAGTCG
Found at i:1191171 original size:2 final size:2
Alignment explanation
Indices: 1191164--1191188 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1191154 TGTGAAAAGA
1191164 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1191189 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1197148 original size:116 final size:116
Alignment explanation
Indices: 1196939--1197255 Score: 616
Period size: 116 Copynumber: 2.7 Consensus size: 116
1196929 ATAAATAGGT
1196939 ATTCTACAAAGCATATGCATCATCATTGAAATAGATGTCTCATTTGCACACTGGTAGTGACATTA
1 ATTCTACAAAGCATATGCATCATCATTGAAATAGATGTCTCATTTGCACACTGGTAGTGACATTA
1197004 ACATCGACAATTTGACATAGATGCCTCATTTGTATTATCCCTTGAATTTGC
66 ACATCGACAATTTGACATAGATGCCTCATTTGTATTATCCCTTGAATTTGC
1197055 ATTCTACAAAGCATATGCATCATCATTGAAATAGATGTCTCATTTGCACACTGGTAGTGACATTA
1 ATTCTACAAAGCATATGCATCATCATTGAAATAGATGTCTCATTTGCACACTGGTAGTGACATTA
*
1197120 ACATCGACAATTTGACATAGATGTCTCATTTGTATTATCCCTTGAATTTGC
66 ACATCGACAATTTGACATAGATGCCTCATTTGTATTATCCCTTGAATTTGC
*
1197171 ATTCTACAAAGCATATCCATCATCATTGAAATAGATGTCTCATTTGCACACTGGTAGTGACATTA
1 ATTCTACAAAGCATATGCATCATCATTGAAATAGATGTCTCATTTGCACACTGGTAGTGACATTA
1197236 ACATCGACAATTTGACATAG
66 ACATCGACAATTTGACATAG
1197256 GTATTCGCAC
Statistics
Matches: 199, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 199 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (116 bp):
ATTCTACAAAGCATATGCATCATCATTGAAATAGATGTCTCATTTGCACACTGGTAGTGACATTA
ACATCGACAATTTGACATAGATGCCTCATTTGTATTATCCCTTGAATTTGC
Found at i:1197814 original size:2 final size:2
Alignment explanation
Indices: 1197807--1197842 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1197797 TTTAAATTAA
1197807 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1197843 TTTAGATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1204776 original size:30 final size:30
Alignment explanation
Indices: 1204742--1204830 Score: 151
Period size: 30 Copynumber: 3.0 Consensus size: 30
1204732 GGTCTAAATC
*
1204742 AGGAATTACAGTGGTTGTAGGATTTTCAGT
1 AGGAATTACAGTGGTTGTAGGATTTTCAAT
* *
1204772 AGGAATTACAGTGGCTATAGGATTTTCAAT
1 AGGAATTACAGTGGTTGTAGGATTTTCAAT
1204802 AGGAATTACAGTGGTTGTAGGATTTTCAA
1 AGGAATTACAGTGGTTGTAGGATTTTCAA
1204831 CAATAGTTGT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (30 bp):
AGGAATTACAGTGGTTGTAGGATTTTCAAT
Found at i:1208957 original size:36 final size:36
Alignment explanation
Indices: 1208910--1208990 Score: 162
Period size: 36 Copynumber: 2.2 Consensus size: 36
1208900 AATCTGGGTT
1208910 TCTTTCAATCTTATAAAGCCTAGGGTTTGCTTTTAA
1 TCTTTCAATCTTATAAAGCCTAGGGTTTGCTTTTAA
1208946 TCTTTCAATCTTATAAAGCCTAGGGTTTGCTTTTAA
1 TCTTTCAATCTTATAAAGCCTAGGGTTTGCTTTTAA
1208982 TCTTTCAAT
1 TCTTTCAAT
1208991 TTCTCCTTAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (36 bp):
TCTTTCAATCTTATAAAGCCTAGGGTTTGCTTTTAA
Found at i:1209202 original size:29 final size:30
Alignment explanation
Indices: 1209160--1209218 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
1209150 GTTTTTAAGT
*
1209160 TTTAGCTGATTTTTTTTAGGTTT-ATTTTAC
1 TTTAGCTGATTTTTGTTA-GTTTAATTTTAC
1209190 TTTAGCTGA-TTTTGTTAGTTTAATTTTAC
1 TTTAGCTGATTTTTGTTAGTTTAATTTTAC
1209219 ATTTTTAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 4 0.15
29 14 0.52
30 9 0.33
ACGTcount: A:0.19, C:0.07, G:0.14, T:0.61
Consensus pattern (30 bp):
TTTAGCTGATTTTTGTTAGTTTAATTTTAC
Found at i:1218772 original size:7 final size:7
Alignment explanation
Indices: 1218762--1218786 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1218752 TTTCAGATTT
1218762 TAGAATA
1 TAGAATA
1218769 TAGAATA
1 TAGAATA
1218776 TAGAATA
1 TAGAATA
1218783 TAGA
1 TAGA
1218787 GAGTAACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (7 bp):
TAGAATA
Found at i:1219988 original size:14 final size:14
Alignment explanation
Indices: 1219971--1220001 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1219961 AATCTAGTAG
1219971 TATTATACATGCAA
1 TATTATACATGCAA
*
1219985 TATTATATATGCAA
1 TATTATACATGCAA
1219999 TAT
1 TAT
1220002 CTTAAATGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (14 bp):
TATTATACATGCAA
Found at i:1220462 original size:19 final size:19
Alignment explanation
Indices: 1220436--1220483 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
1220426 GAAAACTAAT
**
1220436 AAATAAAAA-AATCTAAAA
1 AAATAAAAATAAAATAAAA
*
1220454 AAATAAAAATAAAATAATA
1 AAATAAAAATAAAATAAAA
1220473 AAATAAAAATA
1 AAATAAAAATA
1220484 TAAACTAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (19 bp):
AAATAAAAATAAAATAAAA
Found at i:1220466 original size:14 final size:14
Alignment explanation
Indices: 1220449--1220487 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1220439 TAAAAAAATC
1220449 TAAAAAAATAAAAA
1 TAAAAAAATAAAAA
*
1220463 TAAAATAAT-AAAA
1 TAAAAAAATAAAAA
*
1220476 TAAAAATATAAA
1 TAAAAAAATAAA
1220488 CTAGTTAGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAAAAAATAAAAA
Found at i:1223862 original size:75 final size:75
Alignment explanation
Indices: 1223739--1223889 Score: 275
Period size: 75 Copynumber: 2.0 Consensus size: 75
1223729 GACATGAAGA
* *
1223739 AAGGTTGAAGAAGGGTGTGAAAAGTGTAAAATGAGGCCTTATTTATAATCCTTAAAGGTTAAAGC
1 AAGGTGGAAGAAGGGTGTGAAAAGTGTAAAATGAGGCCTTATTTATAATCCTTAAAGGTCAAAGC
1223804 ATATACCAAT
66 ATATACCAAT
*
1223814 AAGGTGGAAGAAGGGTGTGAAAAGTGTGAAATGAGGCCTTATTTATAATCCTTAAAGGTCAAAGC
1 AAGGTGGAAGAAGGGTGTGAAAAGTGTAAAATGAGGCCTTATTTATAATCCTTAAAGGTCAAAGC
1223879 ATATACCAAT
66 ATATACCAAT
1223889 A
1 A
1223890 GGAAAAATAT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (75 bp):
AAGGTGGAAGAAGGGTGTGAAAAGTGTAAAATGAGGCCTTATTTATAATCCTTAAAGGTCAAAGC
ATATACCAAT
Found at i:1232512 original size:22 final size:22
Alignment explanation
Indices: 1232486--1232536 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1232476 ACTGAAAATA
1232486 AGTATCGGTGCCATAGTATAGT
1 AGTATCGGTGCCATAGTATAGT
1232508 AGTATCGGTGCCATAGTATAGT
1 AGTATCGGTGCCATAGTATAGT
*
1232530 TGTATCG
1 AGTATCG
1232537 ATATTGAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.33
Consensus pattern (22 bp):
AGTATCGGTGCCATAGTATAGT
Found at i:1233081 original size:20 final size:20
Alignment explanation
Indices: 1233056--1233519 Score: 153
Period size: 20 Copynumber: 20.6 Consensus size: 20
1233046 ACTAAAATGT
* *
1233056 ATGAAATGATGTATTAAGGC
1 ATGAAAGGATGCATTAAGGC
1233076 ATGAAAGGATGCATTAAGGC
1 ATGAAAGGATGCATTAAGGC
*
1233096 ATGAAAGGATGCCATAATTATAATGC
1 ATGAAAGGATG-C---A-T-TAAGGC
*
1233122 ATGAACA-GATGCATTAAGGA
1 ATGAA-AGGATGCATTAAGGC
*
1233142 ATGAAAGGATGCCATAACTAAAATGC
1 ATGAAAGGATG-CAT---T--AAGGC
* *
1233168 ATGAAATGTTGCATTAAGGC
1 ATGAAAGGATGCATTAAGGC
*
1233188 ATGAAAGGATGCCATAACTAAAATGC
1 ATGAAAGGATG-CAT---T--AAGGC
*
1233214 ATGAAAGGATGTATTAAGGC
1 ATGAAAGGATGCATTAAGGC
* *
1233234 ATGGAAGGATGCCATAATTATAATGC
1 ATGAAAGGATG-C---A-T-TAAGGC
1233260 ATGAACA-GATGCATTAAGGC
1 ATGAA-AGGATGCATTAAGGC
* *
1233280 ATGAAAGAATGCCATAAATAAAATGC
1 ATGAAAGGATG-CAT---T--AAGGC
*
1233306 ATGAAAGGATGCTTTAAGGC
1 ATGAAAGGATGCATTAAGGC
*
1233326 ATGAAAGGATGCCATAAATAAAATGC
1 ATGAAAGGATG-CAT---T--AAGGC
*
1233352 ATGAAAAGATGCATTAAGG-
1 ATGAAAGGATGCATTAAGGC
** *
1233371 AAAAAAGGATGCCATAATTATAATGC
1 ATGAAAGGATG-C---A-T-TAAGGC
* * *
1233397 ATGAACGAATGCATTCAGGC
1 ATGAAAGGATGCATTAAGGC
*
1233417 ATGAAAGGATGCCATAACTAATATGC
1 ATGAAAGGATG-CAT---T-A-AGGC
1233443 ATGAAAGGATGCATTAAGGC
1 ATGAAAGGATGCATTAAGGC
* *
1233463 ATGAAA-CATGCCATAACTAAAATGC
1 ATGAAAGGATG-CAT---T--AAGGC
*
1233488 ATGAAAGGATGCATTAGGGC
1 ATGAAAGGATGCATTAAGGC
*
1233508 AAGAAAGGATGC
1 ATGAAAGGATGC
1233520 CATGATTAAA
Statistics
Matches: 334, Mismatches: 50, Indels: 120
0.66 0.10 0.24
Matches are distributed among these distances:
19 13 0.04
20 140 0.42
21 19 0.06
22 9 0.03
23 2 0.01
24 8 0.02
25 35 0.10
26 106 0.32
27 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (20 bp):
ATGAAAGGATGCATTAAGGC
Found at i:1233146 original size:46 final size:46
Alignment explanation
Indices: 1233074--1233577 Score: 658
Period size: 46 Copynumber: 11.0 Consensus size: 46
1233064 ATGTATTAAG
* *
1233074 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTATAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
*
1233120 GCATGAACA-GATGCATTAAGGAATGAAAGGATGCCATAACTAAAAT
1 GCATGAA-AGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
* *
1233166 GCATGAAATGTTGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
* * * *
1233212 GCATGAAAGGATGTATTAAGGCATGGAAGGATGCCATAATTATAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
* *
1233258 GCATGAACA-GATGCATTAAGGCATGAAAGAATGCCATAAATAAAAT
1 GCATGAA-AGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
* *
1233304 GCATGAAAGGATGCTTTAAGGCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
* ** * *
1233350 GCATGAAAAGATGCATTAAGG-AAAAAAGGATGCCATAATTATAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
* * * *
1233395 GCATGAACGAATGCATTCAGGCATGAAAGGATGCCATAACTAATAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
*
1233441 GCATGAAAGGATGCATTAAGGCATGAAA-CATGCCATAACTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
* * * *
1233486 GCATGAAAGGATGCATTAGGGCAAGAAAGGATGCCATGATTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
* * * * *
1233532 GCATGAACGGATGTATTAATGCATGAAAAGA-GACCATAACTGAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATG-CCATAACTAAAAT
1233578 TAATGAATAA
Statistics
Matches: 399, Mismatches: 52, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
45 81 0.20
46 316 0.79
47 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (46 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
Found at i:1233323 original size:138 final size:138
Alignment explanation
Indices: 1233074--1233577 Score: 746
Period size: 138 Copynumber: 3.7 Consensus size: 138
1233064 ATGTATTAAG
*
1233074 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTATAATGCATGAACAGATGCATTAA
1 GCATGAAAGGATGCATTAAGGCAAGAAAGGATGCCATAATTATAATGCATGAACAGATGCATTAA
* * *
1233139 GGAATGAAAGGATGCCATAACTAAAATGCATGAAATGTTGCATTAAGGCATGAAAGGATGCCATA
66 GGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
1233204 ACTAAAAT
131 ACTAAAAT
* * *
1233212 GCATGAAAGGATGTATTAAGGCATGGAAGGATGCCATAATTATAATGCATGAACAGATGCATTAA
1 GCATGAAAGGATGCATTAAGGCAAGAAAGGATGCCATAATTATAATGCATGAACAGATGCATTAA
* * *
1233277 GGCATGAAAGAATGCCATAAATAAAATGCATGAAAGGATGCTTTAAGGCATGAAAGGATGCCATA
66 GGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
*
1233342 AATAAAAT
131 ACTAAAAT
* * *
1233350 GCATGAAAAGATGCATTAAGG-AAAAAAGGATGCCATAATTATAATGCATGAAC-GAATGCATTC
1 GCATGAAAGGATGCATTAAGGCAAGAAAGGATGCCATAATTATAATGCATGAACAG-ATGCATTA
* *
1233413 AGGCATGAAAGGATGCCATAACTAATATGCATGAAAGGATGCATTAAGGCATGAAA-CATGCCAT
65 AGGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCAT
1233477 AACTAAAAT
130 AACTAAAAT
* * * * *
1233486 GCATGAAAGGATGCATTAGGGCAAGAAAGGATGCCATGATTAAAATGCATGAACGGATGTATTAA
1 GCATGAAAGGATGCATTAAGGCAAGAAAGGATGCCATAATTATAATGCATGAACAGATGCATTAA
* * *
1233551 TGCATGAAAAGA-GACCATAACTGAAAT
66 GGCATGAAAGGATG-CCATAACTAAAAT
1233578 TAATGAATAA
Statistics
Matches: 330, Mismatches: 32, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
136 36 0.11
137 145 0.44
138 149 0.45
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (138 bp):
GCATGAAAGGATGCATTAAGGCAAGAAAGGATGCCATAATTATAATGCATGAACAGATGCATTAA
GGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
ACTAAAAT
Found at i:1237481 original size:3 final size:3
Alignment explanation
Indices: 1237473--1237513 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
1237463 TAATACTTAT
1237473 TTA TTA TTA TTA TTA TTAA TT- TT- TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
1237514 AATTTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.