Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009289.1 Hibiscus syriacus cultivar Beakdansim tig00112988_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: 1661737
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1097574 original size:9 final size:8
Alignment explanation
Indices: 1097562--1097599 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
1097552 AAAAGGGCAA
1097562 AAAAAAAG
1 AAAAAAAG
1097570 CAAAAAAAG
1 -AAAAAAAG
1097579 AACAAAAAG
1 AA-AAAAAG
1097588 -AAAAAAG
1 AAAAAAAG
1097595 AAAAA
1 AAAAA
1097600 GGGACAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 6 0.22
8 7 0.26
9 14 0.52
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1097577 original size:22 final size:21
Alignment explanation
Indices: 1097551--1097611 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
1097541 TAATCAGAAT
1097551 AAAAAGGGCAAAAAAAAAGCAA-
1 AAAAAGGGCAAAAAAAAA--AAG
**
1097573 AAAAAGAACAAAAAGAAAAAAG
1 AAAAAGGGCAAAAA-AAAAAAG
1097595 AAAAAGGGACAAAAAAA
1 AAAAAGGG-CAAAAAAA
1097612 CACATGCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 2 0.06
22 20 0.62
23 10 0.31
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.00
Consensus pattern (21 bp):
AAAAAGGGCAAAAAAAAAAAG
Found at i:1098227 original size:22 final size:22
Alignment explanation
Indices: 1098199--1098242 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1098189 AGCTACCCCA
1098199 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
1098221 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
1098243 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:1099252 original size:36 final size:36
Alignment explanation
Indices: 1099205--1099467 Score: 272
Period size: 36 Copynumber: 7.4 Consensus size: 36
1099195 ATTGAAAACA
* *
1099205 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
1099241 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* * *
1099278 TTTCTCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * *
1099314 TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
* * *
1099343 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
** * * *
1099379 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* *
1099416 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
1099452 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
1099468 ATCTTTGAAT
Statistics
Matches: 188, Mismatches: 28, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.10
30 2 0.01
35 1 0.01
36 99 0.53
37 65 0.35
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:1099353 original size:102 final size:102
Alignment explanation
Indices: 1099247--1099431 Score: 300
Period size: 102 Copynumber: 1.8 Consensus size: 102
1099237 ATAGTTTCCC
* *
1099247 TTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTT-GAAATAAATTTTGTCTCTCTTGAGA
1 TTGAAAC-AAATTTCGTCTCCCTTGAGACAGTTTCTCTTGGAAATAAATTTTGTCTCTCTTGAGA
1099311 CAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
65 CAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
* * *
1099349 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
1 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGGAAATAAATTTTGTCTCTCTTGAGAC
*
1099414 AGTTTCTCTTGAAACAAA
66 AGTTTCCCTTGAAACAAA
1099432 TTTCGTCTAT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
101 28 0.37
102 48 0.63
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (102 bp):
TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGGAAATAAATTTTGTCTCTCTTGAGAC
AGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
Found at i:1099405 original size:138 final size:138
Alignment explanation
Indices: 1099139--1099529 Score: 500
Period size: 138 Copynumber: 2.8 Consensus size: 138
1099129 ACTCATGATT
* * * * * *
1099139 GTTTTTCTTAAAACAAGA-TTTGTCTCTCTTGAGACAGTTTCTCTCGAAACATAAACA-TTGAAA
1 GTTTCTCTTGAAACAA-ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAATATTTGAAT
* * * *
1099202 ACATTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTC
64 ATATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTC
1099267 TCTTGAGACA
129 TCTTGAGACA
*
1099277 GTTTCTCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATAT
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATAT
* * * ** * * *
1099342 GTTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTC
66 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTC
1099407 TTGAGACA
131 TTGAGACA
* * *
1099415 GTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT-T
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATAT
* * * * *
1099479 ATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
66 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACA
1099530 CAAAATCTTC
Statistics
Matches: 218, Mismatches: 33, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
137 47 0.22
138 171 0.78
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (138 bp):
GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATAT
ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTC
TTGAGACA
Found at i:1099526 original size:64 final size:65
Alignment explanation
Indices: 1099425--1099598 Score: 215
Period size: 64 Copynumber: 2.6 Consensus size: 65
1099415 GTTTCTCTTG
* ** * **
1099425 AAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAA-TTATTTCCCCTA
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
* *
1099489 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
1099554 TA
64 TA
* * *
1099556 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
1099599 CATATATTTT
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
64 31 0.33
65 2 0.02
66 16 0.17
67 18 0.19
68 27 0.29
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:1099581 original size:68 final size:66
Alignment explanation
Indices: 1099425--1099597 Score: 215
Period size: 68 Copynumber: 2.6 Consensus size: 66
1099415 GTTTCTCTTG
* ** * **
1099425 AAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTATTTCCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTATTTCCCCT
1099488 A
66 A
* *
1099489 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAA-TTATTTCCCC
1099554 TA
65 TA
* * *
1099556 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1099598 ACATATATTT
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
64 31 0.33
65 2 0.02
66 12 0.13
67 16 0.17
68 32 0.34
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (66 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTATTTCCCCT
A
Found at i:1100363 original size:105 final size:105
Alignment explanation
Indices: 1100202--1100651 Score: 694
Period size: 105 Copynumber: 4.3 Consensus size: 105
1100192 GCCATCCGCG
* * * *
1100202 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACGCAAGTTCAACTTCACGACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
1100267 GGGACCGCTGCTTGTCAACAACAACTTCTCAATTTTAGAGCCA
63 GGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
*
1100310 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1100375 ACCGCTGCTTGTCAACAACAACTTCCCAATCGCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
*
1100415 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1100480 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
1100520 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * **
1100585 ACCGTTGCTTGTCAACAA-AA-TT-TC-AT-TCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* *
1100620 ATTTCAACTTCACGACGGAGGATATTGGACTC
1 ATTTCAACTTCACAACGAAGGATATTGGACTC
1100652 TGAACAATGC
Statistics
Matches: 323, Mismatches: 19, Indels: 8
0.92 0.05 0.02
Matches are distributed among these distances:
100 37 0.11
101 2 0.01
102 1 0.00
103 2 0.01
104 2 0.01
105 254 0.79
106 3 0.01
108 22 0.07
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
Found at i:1101812 original size:12 final size:11
Alignment explanation
Indices: 1101795--1101882 Score: 54
Period size: 12 Copynumber: 7.4 Consensus size: 11
1101785 TTATTATGGA
1101795 TATTTTATTCAT
1 TATTTTATT-AT
1101807 TATTTTTATTAT
1 TA-TTTTATTAT
*
1101819 TCATGTTATTAT
1 T-ATTTTATTAT
*
1101831 TATATATATTAAAT
1 TAT-TTTATT--AT
1101845 TATTTTCATT-T
1 TATTTT-ATTAT
*
1101856 GATTTT-TTACT
1 TATTTTATTA-T
1101867 ATATTTTATTAT
1 -TATTTTATTAT
1101879 TATT
1 TATT
1101883 ATATATATTT
Statistics
Matches: 60, Mismatches: 6, Indels: 21
0.69 0.07 0.24
Matches are distributed among these distances:
9 2 0.03
11 13 0.22
12 24 0.40
13 13 0.22
14 8 0.13
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:1103120 original size:43 final size:41
Alignment explanation
Indices: 1103061--1103493 Score: 370
Period size: 43 Copynumber: 10.1 Consensus size: 41
1103051 TATATTTATA
* *
1103061 TATAATTGAGATCCCTAATTTTTTCAATCTCACTATTTACCTC
1 TATAATTGA-AGCCCTAATTTTTTCAATCTCACT-TTTACCTT
* * *
1103104 TATAACTGAGGACCCTAATTTTTTCAATCTCACTTTATAGCTT
1 TATAATTGAAG-CCCTAATTTTTTCAATCTCACTTT-TACCTT
*
1103147 TATAATTGAAGCTCCTAATTTTTTCAATCTCACTTTAATAGCTT
1 TATAATTGAAGC-CCTAATTTTTTCAATCTCACTTT--TACCTT
* * * **
1103191 TATAATTGAAACTTCTGATTTTTT-AATCTCACTTTATATTTT
1 TATAATTGAAGC-CCTAATTTTTTCAATCTCACTTT-TACCTT
* *
1103233 TATAATTGAAGCCCCTATTTTTTTTCAATCTCACCTTTTACATT
1 TATAATTGAAG-CCCTA-ATTTTTTCAATCTCA-CTTTTACCTT
* * *
1103277 TATAATTGAGGCCCTAATTTTTTTAATCTCACTTTTTAACTT
1 TATAATTGAAGCCCTAATTTTTTCAATCTCAC-TTTTACCTT
* ** * *
1103319 TACAATTG-AGACATTTAATTTTTTCAATCCCACCTTTTACATT
1 TATAATTGAAG-C-CCTAATTTTTTCAATCTCA-CTTTTACCTT
* * *
1103362 TATAATTAAAGCCCCTGAATTTTTT-AATCTAACTTCTTACATT
1 TATAATTGAAG-CCCT-AATTTTTTCAATCTCACTT-TTACCTT
* *
1103405 TATAATTGAAGCCCTTGATTTTTTTCAATCTCACTTTTTACTTT
1 TATAATTGAAGCCC-T-AATTTTTTCAATCTCAC-TTTTACCTT
* *
1103449 TATAATTGAGGTGCCTAATTTTTT-AATCTCACTTTTTACCTT
1 TATAATTGAAG-CCCTAATTTTTTCAATCTCAC-TTTTACCTT
1103491 TAT
1 TAT
1103494 GAATGAGACT
Statistics
Matches: 325, Mismatches: 46, Indels: 39
0.79 0.11 0.10
Matches are distributed among these distances:
41 2 0.01
42 74 0.23
43 156 0.48
44 85 0.26
45 8 0.02
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (41 bp):
TATAATTGAAGCCCTAATTTTTTCAATCTCACTTTTACCTT
Found at i:1103176 original size:86 final size:83
Alignment explanation
Indices: 1103061--1103546 Score: 398
Period size: 86 Copynumber: 5.7 Consensus size: 83
1103051 TATATTTATA
* * * *
1103061 TATAATTG-AGATCCCTAATTTTTTCAATCTCACTATTTACCTCTATAACTGAGGACCCTAATTT
1 TATAATTGAAGCT-CCTAATTTTTTCAATCTCACT-TTTACATTTATAATTGAGGACCCTAATTT
1103125 TTTCAATCTCACTTTATAGCTT
64 TTT-AATCTCACTTTATA-CTT
* * *
1103147 TATAATTGAAGCTCCTAATTTTTTCAATCTCACTTTAATAGC-TTTATAATTGA-AACTTCTGAT
1 TATAATTGAAGCTCCTAATTTTTTCAATCTCACTTT--TA-CATTTATAATTGAGGAC-CCTAAT
*
1103210 TTTTTAATCTCACTTTATATTTT
62 TTTTTAATCTCACTTTATA-CTT
* *
1103233 TATAATTGAAGCCCCTATTTTTTTTCAATCTCACCTTTTACATTTATAATTGAGG-CCCTAATTT
1 TATAATTGAAGCTCCTA-ATTTTTTCAATCTCA-CTTTTACATTTATAATTGAGGACCCTAA-TT
*
1103297 TTTTAATCTCACTTTTTAACTT
63 TTTTAATCTCACTTTAT-ACTT
* * * * * *
1103319 TACAATTG-AGACAT-TTAATTTTTTCAATCCCACCTTTTACATTTATAATTAAAGCCCCTGAAT
1 TATAATTGAAG-C-TCCTAATTTTTTCAATCTCA-CTTTTACATTTATAATTGAGGACCCT-AAT
*
1103382 TTTTTAATCTAACTTCT-TACATT
62 TTTTTAATCTCACTT-TATAC-TT
* * **
1103405 TATAATTGAAGC-CCTTGATTTTTTTCAATCTCACTTTTTACTTTTATAATTGAGGTGCCTAATT
1 TATAATTGAAGCTCC-T-AATTTTTTCAATCTCAC-TTTTACATTTATAATTGAGGACCCTAATT
*
1103469 TTTTAATCTCACTTTTTACCTT
63 TTTTAATCTCACTTTATA-CTT
** * * * * *
1103491 TATGAA-TG-AGACTTTTAATTTTTCCAATTTAACTTTTTACTTTTATAATTTAGGAC
1 TAT-AATTGAAG-CTCCTAATTTTTTCAATCTCAC-TTTTACATTTATAATTGAGGAC
1103547 TATAATTTAA
Statistics
Matches: 331, Mismatches: 42, Indels: 55
0.77 0.10 0.13
Matches are distributed among these distances:
85 79 0.24
86 167 0.50
87 80 0.24
88 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.48
Consensus pattern (83 bp):
TATAATTGAAGCTCCTAATTTTTTCAATCTCACTTTTACATTTATAATTGAGGACCCTAATTTTT
TAATCTCACTTTATACTT
Found at i:1103538 original size:172 final size:169
Alignment explanation
Indices: 1103079--1103540 Score: 529
Period size: 172 Copynumber: 2.7 Consensus size: 169
1103069 AGATCCCTAA
* * * * * *
1103079 TTTTTTCAATCTCACTATTTACCTCTATAACTGAGGACCCTAATTTTTTCAATCTCACTTTATAG
1 TTTTTTCAATCTCACTTTTTACATTTATAATTGAGG-CCCTAATTTTTT-AATCTCACTTTTTAA
** * **
1103144 CTTTATAATTGA-AGCTCCTAATTTTTTCAATCTCACTTTAATAGCTTTATAATTGAAACTTCTG
64 CTTTATAATTGAGA-CTTTTAATTTTTTCAATCTCACTTT-TTA-CTTTATAATTGAAACCCCTG
* **
1103208 ATTTTTTAATCTCACTTTATATTTTTATAATTGAAGCCCCTATT
126 ATTTTTTAATCTAACTTTATACATTTATAATTGAAGCCCCTATT
*
1103252 TTTTTTCAATCTCACCTTTTACATTTATAATTGAGGCCCTAATTTTTTTAATCTCACTTTTTAAC
1 TTTTTTCAATCTCACTTTTTACATTTATAATTGAGGCCCTAA-TTTTTTAATCTCACTTTTTAAC
* * * *
1103317 TTTACAATTGAGACATTTAATTTTTTCAATCCCACCTTTTACATTTATAATT-AAAGCCCCTGAA
65 TTTATAATTGAGACTTTTAATTTTTTCAATCTCACTTTTTAC-TTTATAATTGAAA-CCCCTG-A
*
1103381 TTTTTTAATCTAACTTCT-TACATTTATAATTGAAGCCCTTGA-T
127 TTTTTTAATCTAACTT-TATACATTTATAATTGAAGCCCCT-ATT
* * *
1103424 TTTTTTCAATCTCACTTTTTACTTTTATAATTGAGGTGCCTAATTTTTTAATCTCACTTTTTACC
1 TTTTTTCAATCTCACTTTTTACATTTATAATTGAGG-CCCTAATTTTTTAATCTCACTTTTTAAC
* * *
1103489 TTTATGAA-TGAGACTTTTAATTTTTCCAATTTAACTTTTTACTTTTATAATT
65 TTTAT-AATTGAGACTTTTAATTTTTTCAATCTCACTTTTTAC-TTTATAATT
1103541 TAGGACTATA
Statistics
Matches: 248, Mismatches: 32, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
170 4 0.02
171 15 0.06
172 182 0.73
173 47 0.19
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.49
Consensus pattern (169 bp):
TTTTTTCAATCTCACTTTTTACATTTATAATTGAGGCCCTAATTTTTTAATCTCACTTTTTAACT
TTATAATTGAGACTTTTAATTTTTTCAATCTCACTTTTTACTTTATAATTGAAACCCCTGATTTT
TTAATCTAACTTTATACATTTATAATTGAAGCCCCTATT
Found at i:1103553 original size:43 final size:42
Alignment explanation
Indices: 1103080--1103554 Score: 171
Period size: 43 Copynumber: 11.1 Consensus size: 42
1103070 GATCCCTAAT
* * * * * **
1103080 TTTTTCAATCTCACTATTTACCTCTATAACTGAGGACCCTAA
1 TTTTTCAATCTAACTTTTTACTTTTATAATTGAGGACTATAA
* * * *
1103122 TTTTTTCAATCTCACTTTATAGC-TTTATAATTGAAG-CTCCTAA
1 -TTTTTCAATCTAACTTTTTA-CTTTTATAATTGAGGACT-ATAA
* * * * *
1103165 TTTTTTCAATCTCACTTTAATAGC-TTTATAATTGA-AACTTCTGA
1 -TTTTTCAATCTAACTTT-TTA-CTTTTATAATTGAGGAC-TATAA
* * * * ** **
1103209 TTTTTTAATCTCACTTTATATTTTTATAATTGAAGCCCCTATTT
1 TTTTTCAATCTAACTTTTTACTTTTATAATTG-AG-GACTATAA
* * * * *
1103253 TTTTTCAATCTCACCTTTTACATTTATAATTGAGGCCCTA-AT
1 TTTTTCAATCTAACTTTTTACTTTTATAATTGAGG-ACTATAA
* * * *
1103295 TTTTTTAATCTCACTTTTTAAC-TTTACAATTGA-GACATTTAA
1 TTTTTCAATCTAACTTTTT-ACTTTTATAATTGAGGAC-TATAA
** * * * * * **
1103337 TTTTTTCAATCCCACCTTTTACATTTATAATTAAAGCCCCTGAA
1 -TTTTTCAATCTAACTTTTTACTTTTATAATTGAGGACTAT-AA
* * * ** *
1103381 TTTTTTAATCTAACTTCTTACATTTATAATTGAAGCCCT-TGATT
1 TTTTTCAATCTAACTTTTTACTTTTATAATTG-AGGACTAT-A-A
* * *
1103425 TTTTTCAATCTCACTTTTTACTTTTATAATTGAGGTGC-CTAA
1 TTTTTCAATCTAACTTTTTACTTTTATAATTGAGG-ACTATAA
* * * *
1103467 TTTTTTAATCTCACTTTTTACCTTTATGAA-TGA-GACTTTTAA
1 TTTTTCAATCTAACTTTTTACTTTTAT-AATTGAGGAC-TATAA
* *
1103509 TTTTTCCAATTTAACTTTTTACTTTTATAATTTAGGACTATAA
1 TTTTT-CAATCTAACTTTTTACTTTTATAATTGAGGACTATAA
1103552 TTT
1 TTT
1103555 AATCATTTTT
Statistics
Matches: 342, Mismatches: 63, Indels: 54
0.75 0.14 0.12
Matches are distributed among these distances:
40 2 0.01
41 3 0.01
42 83 0.24
43 162 0.47
44 90 0.26
45 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (42 bp):
TTTTTCAATCTAACTTTTTACTTTTATAATTGAGGACTATAA
Found at i:1109265 original size:8 final size:8
Alignment explanation
Indices: 1109245--1109293 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
1109235 AAGTAATGAA
1109245 ATAAATA-
1 ATAAATAT
1109252 ATAAATAT
1 ATAAATAT
1109260 ATAAAT-T
1 ATAAATAT
1109267 A-AGAATAT
1 ATA-AATAT
*
1109275 ATATATAT
1 ATAAATAT
*
1109283 ATATATAT
1 ATAAATAT
1109291 ATA
1 ATA
1109294 TCTATCTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
6 1 0.03
7 12 0.32
8 23 0.62
9 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (8 bp):
ATAAATAT
Found at i:1116940 original size:17 final size:17
Alignment explanation
Indices: 1116918--1116952 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1116908 CCTAACGTTT
1116918 GTAACGTTACTATTTTA
1 GTAACGTTACTATTTTA
1116935 GTAACGTTACTATTTTA
1 GTAACGTTACTATTTTA
1116952 G
1 G
1116953 GTGCATATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (17 bp):
GTAACGTTACTATTTTA
Found at i:1117439 original size:23 final size:22
Alignment explanation
Indices: 1117397--1117445 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
1117387 GGGTTATTTC
* *
1117397 AAAATTTATGTTTTTCTTTTTT
1 AAAATATATGTTTTTCTTTTTA
1117419 AAAATATATAGTTTTAT-TTTTTA
1 AAAATATAT-GTTTT-TCTTTTTA
1117442 AAAA
1 AAAA
1117446 ATTTTATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.35
23 14 0.61
24 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (22 bp):
AAAATATATGTTTTTCTTTTTA
Found at i:1119708 original size:18 final size:18
Alignment explanation
Indices: 1119685--1119719 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1119675 AATGTAAGAT
*
1119685 TACCGTGTTTGGTTAAAA
1 TACCGTGTTTGATTAAAA
1119703 TACCGTGTTTGATTAAA
1 TACCGTGTTTGATTAAA
1119720 GAAATAAAAG
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:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (18 bp):
TACCGTGTTTGATTAAAA
Found at i:1120143 original size:41 final size:41
Alignment explanation
Indices: 1120097--1120181 Score: 143
Period size: 41 Copynumber: 2.1 Consensus size: 41
1120087 GGTAGACAAT
* * *
1120097 TCATAATTATGATTGCCGGAGATCTTCTACGAAAATTGCTC
1 TCATAATTATGACTGCCGGAGATCTTCTAAGAAAACTGCTC
1120138 TCATAATTATGACTGCCGGAGATCTTCTAAGAAAACTGCTC
1 TCATAATTATGACTGCCGGAGATCTTCTAAGAAAACTGCTC
1120179 TCA
1 TCA
1120182 ACCTCCTACT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (41 bp):
TCATAATTATGACTGCCGGAGATCTTCTAAGAAAACTGCTC
Found at i:1121676 original size:3 final size:3
Alignment explanation
Indices: 1121668--1121711 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1121658 GAGTAGAGTT
1121668 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1121712 GGAGGTGAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1124540 original size:19 final size:22
Alignment explanation
Indices: 1124501--1124540 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
1124491 CATCAGTAAA
1124501 TAATTCATATTTAATTTAATGT
1 TAATTCATATTTAATTTAATGT
1124523 TAATT-ATA-TTAA-TTAATG
1 TAATTCATATTTAATTTAATG
1124541 GCCAAAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 3 0.17
22 5 0.28
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (22 bp):
TAATTCATATTTAATTTAATGT
Found at i:1125146 original size:23 final size:24
Alignment explanation
Indices: 1125119--1125167 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1125109 CAAAATCTAA
*
1125119 AAAAAAAACCAAACACC-ATTTTTT
1 AAAAGAAACCAAAC-CCTATTTTTT
*
1125143 AAAAGAACCCAAACCCTATTTTTT
1 AAAAGAAACCAAACCCTATTTTTT
1125167 A
1 A
1125168 GATCTAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.49, C:0.22, G:0.02, T:0.27
Consensus pattern (24 bp):
AAAAGAAACCAAACCCTATTTTTT
Found at i:1126651 original size:19 final size:20
Alignment explanation
Indices: 1126627--1126680 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
1126617 TCGATGCACA
*
1126627 GTGCATGGATGCACTGCA-G
1 GTGCATGGATGCACTACAGG
*
1126646 GTGCATAGATGCACTACAGG
1 GTGCATGGATGCACTACAGG
1126666 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1126681 TTGACACCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.22
Consensus pattern (20 bp):
GTGCATGGATGCACTACAGG
Found at i:1126920 original size:21 final size:21
Alignment explanation
Indices: 1126896--1126940 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1126886 AATAAAATGT
1126896 TTAACGAAAA-AATATCAATTG
1 TTAA-GAAAATAATATCAATTG
* *
1126917 TTAATAAAATGATATCAATTG
1 TTAAGAAAATAATATCAATTG
1126938 TTA
1 TTA
1126941 CCAATTGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.36
Consensus pattern (21 bp):
TTAAGAAAATAATATCAATTG
Found at i:1128660 original size:14 final size:14
Alignment explanation
Indices: 1128619--1128658 Score: 71
Period size: 14 Copynumber: 2.8 Consensus size: 14
1128609 TTTCTTCTTC
1128619 TCTTCTCTTCCCTT
1 TCTTCTCTTCCCTT
1128633 TCTTCTCTTCCCTT
1 TCTTCTCTTCCCTT
1128647 TCTTCATCTTCC
1 TCTTC-TCTTCC
1128659 TTCACCATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.03, C:0.42, G:0.00, T:0.55
Consensus pattern (14 bp):
TCTTCTCTTCCCTT
Found at i:1139262 original size:32 final size:32
Alignment explanation
Indices: 1139201--1139263 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
1139191 GGACCAACTT
** *
1139201 TATTTTAATTTATTATTAAGTTAATAATAAAA
1 TATTTTAATAAATTATTAAATTAATAATAAAA
1139233 TATTTTAATAAATATATTAAATTAA-AATAAA
1 TATTTTAATAAAT-TATTAAATTAATAATAAA
1139264 GTTAGTCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (32 bp):
TATTTTAATAAATTATTAAATTAATAATAAAA
Found at i:1141059 original size:21 final size:21
Alignment explanation
Indices: 1141027--1141087 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
1141017 GAAGTTACTG
*
1141027 TAGCAGTACATCGGTACACTA
1 TAGCAGTGCATCGGTACACTA
* *
1141048 TAGCATTGCATCGGTACACTG
1 TAGCAGTGCATCGGTACACTA
*
1141069 TAGCAGTGCATCGATACAC
1 TAGCAGTGCATCGGTACAC
1141088 AATTTATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (21 bp):
TAGCAGTGCATCGGTACACTA
Found at i:1141133 original size:21 final size:21
Alignment explanation
Indices: 1141109--1141149 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1141099 AATGTTTTTG
*
1141109 TGCATCGATATACTGTAGCAA
1 TGCATCGATAGACTGTAGCAA
* *
1141130 TGCATTGGTAGACTGTAGCA
1 TGCATCGATAGACTGTAGCA
1141150 CTGTTCATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCATCGATAGACTGTAGCAA
Found at i:1142009 original size:23 final size:23
Alignment explanation
Indices: 1141983--1142046 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 23
1141973 AATCTTATAT
*
1141983 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
1142006 GGCACTTCGGTACATATTCTACGT
1 GGCACTTCGGTGCA-ATTCTACGC
*
1142030 GGCACTTTGGTGCAATT
1 GGCACTTCGGTGCAATT
1142047 TATACGAGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 15 0.43
24 20 0.57
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:1142398 original size:25 final size:25
Alignment explanation
Indices: 1142369--1142420 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1142359 ATATTTAATT
1142369 ATATGAATATATTTAATTATATGAA
1 ATATGAATATATTTAATTATATGAA
1142394 ATATGAATATATTTAATTATATGAA
1 ATATGAATATATTTAATTATATGAA
1142419 AT
1 AT
1142421 GTTATATGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (25 bp):
ATATGAATATATTTAATTATATGAA
Found at i:1142418 original size:18 final size:18
Alignment explanation
Indices: 1142351--1142397 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1142341 TGAGTTATGC
*
1142351 ATATAAATATATTTAATT
1 ATATGAATATATTTAATT
1142369 ATATGAATATATTTAATT
1 ATATGAATATATTTAATT
1142387 ATATGAA-ATAT
1 ATATGAATATAT
1142398 GAATATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 4 0.14
18 24 0.86
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (18 bp):
ATATGAATATATTTAATT
Found at i:1144524 original size:45 final size:46
Alignment explanation
Indices: 1144474--1144573 Score: 132
Period size: 44 Copynumber: 2.2 Consensus size: 46
1144464 CTATTTTTTT
* *
1144474 AATATTTACATTAGAACACTACTTAAAATATTA-TTTTTCTACC-GA
1 AATATTAACATCAG-ACACTACTTAAAATATTATTTTTTCTACCGGA
* *
1144519 AATATTAATATCAGACGCTACTTAAAATATTATTTTTTTCTACCGGA
1 AATATTAACATCAGACACTACTTAAAATATTA-TTTTTTCTACCGGA
1144566 AATATTAA
1 AATATTAA
1144574 TATTGGAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
44 17 0.35
45 11 0.23
46 10 0.21
47 10 0.21
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (46 bp):
AATATTAACATCAGACACTACTTAAAATATTATTTTTTCTACCGGA
Found at i:1144640 original size:22 final size:21
Alignment explanation
Indices: 1144587--1144640 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
1144577 TGGAAATATT
* *
1144587 CATTTTAGATAGTAAAGTTAA
1 CATTTTAGATAGAAAAATTAA
**
1144608 CATTTCCGATAGAAAAAATTAA
1 CATTTTAGATAG-AAAAATTAA
*
1144630 TATTTTAGATA
1 CATTTTAGATA
1144641 ACGCTCTACC
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (21 bp):
CATTTTAGATAGAAAAATTAA
Found at i:1153119 original size:22 final size:22
Alignment explanation
Indices: 1153093--1153137 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1153083 TTAAACCCCA
1153093 CTAAACCTCTTTCTATGGCCAC
1 CTAAACCTCTTTCTATGGCCAC
1153115 CTAAACCTCTTTCTATGGCCAC
1 CTAAACCTCTTTCTATGGCCAC
1153137 C
1 C
1153138 ATAGCCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.38, G:0.09, T:0.31
Consensus pattern (22 bp):
CTAAACCTCTTTCTATGGCCAC
Found at i:1156007 original size:39 final size:35
Alignment explanation
Indices: 1155947--1156028 Score: 110
Period size: 39 Copynumber: 2.2 Consensus size: 35
1155937 AACTTAACAT
1155947 TAAACTTTGAATGGGGTACTAAAATGAAACGAAAAC
1 TAAACTTTGAATGGGGTACTAAAATGAAAC-AAAAC
*
1155983 TAAAGCTTTTAATGGTGGATACTAAAATGAAACAAAAC
1 TAAA-CTTTGAATGG-GG-TACTAAAATGAAACAAAAC
*
1156021 TACACTTT
1 TAAACTTT
1156029 AGGTATGATT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
36 4 0.10
37 13 0.32
38 10 0.24
39 14 0.34
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (35 bp):
TAAACTTTGAATGGGGTACTAAAATGAAACAAAAC
Found at i:1156841 original size:35 final size:35
Alignment explanation
Indices: 1156794--1156860 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
1156784 CACCACCTAT
1156794 ATACATAGATAACAAACTAAGAACATATATATGTC
1 ATACATAGATAACAAACTAAGAACATATATATGTC
* * *
1156829 ATACATATATAACGAATTAAGAACATATATAT
1 ATACATAGATAACAAACTAAGAACATATATAT
1156861 ATAAGTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.28
Consensus pattern (35 bp):
ATACATAGATAACAAACTAAGAACATATATATGTC
Found at i:1165781 original size:22 final size:22
Alignment explanation
Indices: 1165734--1165781 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1165724 GACCAAAAAT
* *
1165734 AATAAAAATAGTATTTTTATTC
1 AATAAAAATAGTATTTTAATTA
1165756 AATAAAAATAGTGA-TTTAATTA
1 AATAAAAATAGT-ATTTTAATTA
1165778 AATA
1 AATA
1165782 TATATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (22 bp):
AATAAAAATAGTATTTTAATTA
Found at i:1166831 original size:132 final size:134
Alignment explanation
Indices: 1166686--1167094 Score: 518
Period size: 136 Copynumber: 3.0 Consensus size: 134
1166676 TCGAAATTTT
* * * *
1166686 TTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGGTCGATTAACCGAACCGAATT-ATCTAATT
1 TTCGGTTCAGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACCAAATT
* ** * *
1166750 TTTGCTTCGATTAATAATTTTTTCA-AAAAAATTGGTTAATTCGGTTTGG-TAATTAATTTTCAA
66 TTTGCTTCGATTAATAAGTTAATAATAAAAAATCGGTTAATTCGGTTTGGTTAA-TAATTTTCAA
1166813 ATTAA
130 ATTAA
* *
1166818 TTCGGTTCAGTTAATAATTTTCAAATAAATTTTAGTTCGATTAACCGAACCAAATTAACCAAATT
1 TTCGGTTCAGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACCAAATT
**
1166883 TTTGCTTCGATTAATTCGGTTAATAATTAAAAAATCGGTTAATTCGGTTTGGTTAATAATTTTCA
66 TTTGCTTCGATTAA-TAAGTTAATAA-TAAAAAATCGGTTAATTCGGTTTGGTTAATAATTTTCA
1166948 AATTAA
129 AATTAA
* * * *
1166954 TTCAGTTCATTTAATAATTTTCAAATAAATTTTGGTTCGATTAAACGAACCGAATTAACCGAATT
1 TTCGGTTCAGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACCAAATT
* ** *
1167019 TTTGCTTTGATTAATTCGGTTAATAATTTTTAAAAAATCGGTTAATTCAGTTTGGTTAATAATTT
66 TTTGCTTCGATTAA-TAAGTTAATAA----TAAAAAATCGGTTAATTCGGTTTGGTTAATAATTT
* *
1167084 TGAAATAAA
126 TCAAATTAA
1167093 TT
1 TT
1167095 TTAATTCGAT
Statistics
Matches: 246, Mismatches: 23, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
132 52 0.21
133 20 0.08
134 5 0.02
136 122 0.50
137 3 0.01
139 44 0.18
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (134 bp):
TTCGGTTCAGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACCAAATT
TTTGCTTCGATTAATAAGTTAATAATAAAAAATCGGTTAATTCGGTTTGGTTAATAATTTTCAAA
TTAA
Found at i:1166835 original size:29 final size:29
Alignment explanation
Indices: 1166785--1166848 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
1166775 AAAAAATTGG
*
1166785 TTAATTCGGTTTGGTAATTAATTTTCAAA
1 TTAATTCGGTTAGGTAATTAATTTTCAAA
*
1166814 TTAATTCGGTTCAGTTAA-TAATTTTCAAA
1 TTAATTCGGTT-AGGTAATTAATTTTCAAA
*
1166843 TAAATT
1 TTAATT
1166849 TTAGTTCGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (29 bp):
TTAATTCGGTTAGGTAATTAATTTTCAAA
Found at i:1167078 original size:110 final size:112
Alignment explanation
Indices: 1166950--1167209 Score: 296
Period size: 110 Copynumber: 2.3 Consensus size: 112
1166940 AATTTTCAAA
* ** *
1166950 TTAATTCAG-TTCATTTAATAATTTTCAAATAAATTTTGGTTCGATTAAACGAACCGAATTAACC
1 TTAATTCAGTTTGA-TTAATAATTTTCAAATAAATTTTAATTCGATTAAACAAACCGAATTAACC
* * *
1167014 -GAATTTTTGCTTTGATTAATTCGGTTAATAATTTT-TA-AAAAATCGG
65 AAAATTTTT-CTTCGATTAATTCGGTTAATAATTTTAAATAAAAATCGG
* * * **
1167060 TTAATTCAGTTTGGTTAATAATTTTGAAATAAATTTTAATTCGATTAACCAAATTGAATTAACCA
1 TTAATTCAGTTTGATTAATAATTTTCAAATAAATTTTAATTCGATTAAACAAACCGAATTAACCA
*
1167125 AAATTTTTCTTCGATTAATTCGGTTCATAATTTTCAAAAATAAAAATCGG
66 AAATTTTTCTTCGATTAATTCGGTTAATAATTTT---AAATAAAAATCGG
* *
1167175 CTAATTCA-TTTCGATTAATAATTTTCAAATTAATT
1 TTAATTCAGTTT-GATTAATAATTTTCAAATAAATT
1167210 CGATTCAGTT
Statistics
Matches: 125, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
110 76 0.61
111 9 0.07
114 4 0.03
115 36 0.29
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (112 bp):
TTAATTCAGTTTGATTAATAATTTTCAAATAAATTTTAATTCGATTAAACAAACCGAATTAACCA
AAATTTTTCTTCGATTAATTCGGTTAATAATTTTAAATAAAAATCGG
Found at i:1167122 original size:246 final size:249
Alignment explanation
Indices: 1166827--1167280 Score: 650
Period size: 254 Copynumber: 1.8 Consensus size: 249
1166817 ATTCGGTTCA
* *
1166827 GTTAATAATTTTCAAATAAATTTTAGTTCGATTAACCGAACCAAATTAACC-AAATTTTTGCTTC
1 GTTAATAATTTTCAAATAAATTTTAATTCGATTAACCAAACCAAATTAACCAAAATTTTT-CTTC
* * *
1166891 GATTAATTCGGTTAATAA-TT-A-AAAAATCGGTTAATTCGGTTT-GGTTAATAATTTTCAAATT
65 GATTAATTCGGTTAATAATTTAATAAAAATCGGCTAATTC-ATTTCGATTAATAATTTTCAAATT
* * *
1166952 AATTC-AGTTCATTTAATAATTTTCAAATAAATTTTGGTTCGATTAAACGAACCGAATTAACCGA
129 AATTCGA-TTCAGTTAATAATTTTCAAATAAATTTTGGTTCGATTAAACAAACCGAATTAAACGA
1167016 ATTTTTGCTTTGATTAATTCGGTTAATAATTTTTAAAAAATCGGTTAATTCAGTTTG
193 ATTTTTGCTTTGATTAATTCGGTTAATAATTTTTAAAAAATCGGTTAATTCAGTTTG
* ***
1167073 GTTAATAATTTTGAAATAAATTTTAATTCGATTAACCAAATTGAATTAACCAAAATTTTTCTTCG
1 GTTAATAATTTTCAAATAAATTTTAATTCGATTAACCAAACCAAATTAACCAAAATTTTTCTTCG
*
1167138 ATTAATTCGGTTCATAATTTTCAAAAATAAAAATCGGCTAATTCATTTCGATTAATAATTTTCAA
66 ATTAATTCGGTTAATAA-TTT----AATAAAAATCGGCTAATTCATTTCGATTAATAATTTTCAA
* *
1167203 ATTAATTCGATTCAGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCAAACTGAATTAAAC
126 ATTAATTCGATTCAGTTAATAATTTTCAAATAAATTTTGGTTCGATTAAACAAACCGAATTAAAC
*
1167268 GAATTTTTTCTTT
191 GAATTTTTGCTTT
1167281 AACCGTTAAT
Statistics
Matches: 181, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
246 66 0.36
247 8 0.04
248 2 0.01
253 4 0.02
254 100 0.55
255 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (249 bp):
GTTAATAATTTTCAAATAAATTTTAATTCGATTAACCAAACCAAATTAACCAAAATTTTTCTTCG
ATTAATTCGGTTAATAATTTAATAAAAATCGGCTAATTCATTTCGATTAATAATTTTCAAATTAA
TTCGATTCAGTTAATAATTTTCAAATAAATTTTGGTTCGATTAAACAAACCGAATTAAACGAATT
TTTGCTTTGATTAATTCGGTTAATAATTTTTAAAAAATCGGTTAATTCAGTTTG
Found at i:1167844 original size:29 final size:30
Alignment explanation
Indices: 1167777--1167853 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
1167767 AAATTAACGG
* * *
1167777 TCGGTGGTTTGATTAAATCAATTAAATAGT
1 TCGGTGGTCTGATTGATTCAATTAAATAGT
* *
1167807 TGGGTGGTCTGATTGATTCAATTGAA-AGT
1 TCGGTGGTCTGATTGATTCAATTAAATAGT
**
1167836 TCGGTGGTCACATTGATT
1 TCGGTGGTCTGATTGATT
1167854 TTTGACCATA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 18 0.46
30 21 0.54
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (30 bp):
TCGGTGGTCTGATTGATTCAATTAAATAGT
Found at i:1172935 original size:22 final size:21
Alignment explanation
Indices: 1172910--1172953 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1172900 ATTCAAATAG
*
1172910 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGA-TACCCTGCTACA
**
1172932 GGGAATTGATACCCTGCTACA
1 GGGAACCGATACCCTGCTACA
1172953 G
1 G
1172954 TACTTCCGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.20
Consensus pattern (21 bp):
GGGAACCGATACCCTGCTACA
Found at i:1181625 original size:16 final size:16
Alignment explanation
Indices: 1181604--1181636 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1181594 TTTTATTTTG
*
1181604 ATAAAATAATTTTAAA
1 ATAAAATAAGTTTAAA
1181620 ATAAAATAAGTTTAAA
1 ATAAAATAAGTTTAAA
1181636 A
1 A
1181637 ACTTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
ATAAAATAAGTTTAAA
Found at i:1186533 original size:27 final size:29
Alignment explanation
Indices: 1186480--1186533 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
1186470 AGGGGTGAAT
* * *
1186480 TTGAATTTTTAAAAATTTTAGGGGAGAAC
1 TTGAATTTATAAAAATTTCAGGAGAGAAC
1186509 TTGAATTTAT-AAAATTTCA-GAGAGA
1 TTGAATTTATAAAAATTTCAGGAGAGA
1186534 CGAAAATAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.23
28 8 0.36
29 9 0.41
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.37
Consensus pattern (29 bp):
TTGAATTTATAAAAATTTCAGGAGAGAAC
Found at i:1192806 original size:14 final size:14
Alignment explanation
Indices: 1192787--1192821 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1192777 CAAACATCGT
1192787 AAAATGTTTTTCAG
1 AAAATGTTTTTCAG
1192801 AAAATGTTTTTCAG
1 AAAATGTTTTTCAG
1192815 AAAATGT
1 AAAATGT
1192822 AATTCATTTT
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:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (14 bp):
AAAATGTTTTTCAG
Found at i:1195253 original size:7 final size:7
Alignment explanation
Indices: 1195241--1195266 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1195231 GTAATGATGT
1195241 ATTTTAA
1 ATTTTAA
1195248 ATTTTAA
1 ATTTTAA
1195255 ATTTTAA
1 ATTTTAA
1195262 ATTTT
1 ATTTT
1195267 GATTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTTAA
Found at i:1197902 original size:44 final size:44
Alignment explanation
Indices: 1197839--1197927 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
1197829 CTCTCTGGTC
1197839 TTTCTTTCTGGGTTAAATTATGATATTAATCCCTCTACTCGAAG
1 TTTCTTTCTGGGTTAAATTATGATATTAATCCCTCTACTCGAAG
1197883 TTTCTTTCTGGGTTAAATTATGATATTAATCCCTCTACTCGAAG
1 TTTCTTTCTGGGTTAAATTATGATATTAATCCCTCTACTCGAAG
1197927 T
1 T
1197928 AAATTAGCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (44 bp):
TTTCTTTCTGGGTTAAATTATGATATTAATCCCTCTACTCGAAG
Found at i:1207252 original size:18 final size:18
Alignment explanation
Indices: 1207229--1207266 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1207219 AGCATGAATG
1207229 GAGACTCAGTGAGTGAGT
1 GAGACTCAGTGAGTGAGT
*
1207247 GAGACTCAGTGAGTGGGT
1 GAGACTCAGTGAGTGAGT
1207265 GA
1 GA
1207267 AGAGATTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.42, T:0.21
Consensus pattern (18 bp):
GAGACTCAGTGAGTGAGT
Found at i:1210175 original size:23 final size:22
Alignment explanation
Indices: 1210124--1210177 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
1210114 TTTATTCCAT
*
1210124 TCGATTAA-TAATTTTAAAAAA
1 TCGATTAATTAATATTAAAAAA
*
1210145 T-AATTTAATTAATAATTAAAAAA
1 TCGA-TTAATTAAT-ATTAAAAAA
1210168 TCGATTAATT
1 TCGATTAATT
1210178 CAATTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 1 0.04
21 5 0.19
22 4 0.15
23 15 0.58
24 1 0.04
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (22 bp):
TCGATTAATTAATATTAAAAAA
Found at i:1213758 original size:301 final size:301
Alignment explanation
Indices: 1213216--1213814 Score: 1121
Period size: 301 Copynumber: 2.0 Consensus size: 301
1213206 AAATATTGTT
1213216 GGTAAATTACATGTTTAGTACCTAAAGTATTCATTTTTGTTCATTTTAGTACTTAAATTTTTAAT
1 GGTAAATTACATGTTTAGTACCTAAAGTATTCATTTTTGTTCATTTTAGTACTTAAATTTTTAAT
*
1213281 TTTTCAAATCATACATAACGTTTAGTTTTTGTTTCAGCTTAATACTCCGTCGTTAAAAACTTAAT
66 TTTTCAAATCATACATAACATTTAGTTTTTGTTTCAGCTTAATACTCCGTCGTTAAAAACTTAAT
*
1213346 TGGTGGCCTTATTGACTGTCGCATTGTCGGCCGATGAAGGCCAAACTTTCCATCCCACACCTTTT
131 TGGTGGCCTTATCGACTGTCGCATTGTCGGCCGATGAAGGCCAAACTTTCCATCCCACACCTTTT
*
1213411 CGACCACCTGAACATGATTTAGGCCTTCGTTTCACCTACAAATGCATGAATCTCCTCAAATTGAC
196 CGACCACCTGAACATGATTTAGGCCTTCGTTTCACCTACAAATGCATGAATCTCCCCAAATTGAC
*
1213476 TTCTTCATCCTCCGATCTTGACGTCTGAAGGGGTATTTTTG
261 TTCTTCATCCTCCGATCTTGACATCTGAAGGGGTATTTTTG
*
1213517 GGTAAATTACATGTTTAGTACCTAAAGTATTCA-TTTTGTTCGTTTTAGTACTTAAATTTTTAAT
1 GGTAAATTACATGTTTAGTACCTAAAGTATTCATTTTTGTTCATTTTAGTACTTAAATTTTTAA-
1213581 TTTTTCAAATCATACATAACATTTAGTTTTTGTTTCAGCTTAATACTCCGTCGTTAAAAACTTAA
65 TTTTTCAAATCATACATAACATTTAGTTTTTGTTTCAGCTTAATACTCCGTCGTTAAAAACTTAA
1213646 -TGGTGGCCTTATCGACTGTCGCATTTGTCGGCCGATGAAGGCCAAACTTTCCATCCCACACCTT
130 TTGGTGGCCTTATCGACTGTCGCA-TTGTCGGCCGATGAAGGCCAAACTTTCCATCCCACACCTT
1213710 TTCGACCACCTGAACATGATTTAGGCCTTCGTTTCACCTACAAATGCATGAATCTCCCCAAATTG
194 TTCGACCACCTGAACATGATTTAGGCCTTCGTTTCACCTACAAATGCATGAATCTCCCCAAATTG
1213775 ACTTCTTCATCCTCCGATCTTGACATCTGAAGGGGTATTT
259 ACTTCTTCATCCTCCGATCTTGACATCTGAAGGGGTATTT
1213815 AAGTGTTCGT
Statistics
Matches: 291, Mismatches: 5, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
300 51 0.18
301 240 0.82
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (301 bp):
GGTAAATTACATGTTTAGTACCTAAAGTATTCATTTTTGTTCATTTTAGTACTTAAATTTTTAAT
TTTTCAAATCATACATAACATTTAGTTTTTGTTTCAGCTTAATACTCCGTCGTTAAAAACTTAAT
TGGTGGCCTTATCGACTGTCGCATTGTCGGCCGATGAAGGCCAAACTTTCCATCCCACACCTTTT
CGACCACCTGAACATGATTTAGGCCTTCGTTTCACCTACAAATGCATGAATCTCCCCAAATTGAC
TTCTTCATCCTCCGATCTTGACATCTGAAGGGGTATTTTTG
Found at i:1215935 original size:14 final size:14
Alignment explanation
Indices: 1215916--1215946 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1215906 TGATAATATT
1215916 TTAAAATAATTTTA
1 TTAAAATAATTTTA
1215930 TTAAAATAATTTTA
1 TTAAAATAATTTTA
1215944 TTA
1 TTA
1215947 TTACGCCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTAAAATAATTTTA
Found at i:1216889 original size:169 final size:172
Alignment explanation
Indices: 1216654--1216994 Score: 629
Period size: 172 Copynumber: 2.0 Consensus size: 172
1216644 CATGAGCCTG
1216654 CAGCTGAGTGGAGACGGCAAAGAGTTTGGGTTTTTGATATTGATGAGACTCTGTTGTCCAACCTT
1 CAGCTGAGTGGAGACGGCAAAGAGTTTGGGTTTTTGATATTGATGAGACTCTGTTGTCCAACCTT
1216719 CCTTACTACG-TGAGCATGGTTAT-GGTAAGATTTTGATTTGGTCGTTTCC-TTTCTTCTCCAAT
66 CCTTACTACGTTGAGCATGGTTATGGGTAAGATTTTGATTTGGTCGTTTCCTTTTCTTCTCCAAT
1216781 TTTCTTGAACTTGTTTGGTTGCTAAGAAACTGGTAATCTGGT
131 TTTCTTGAACTTGTTTGGTTGCTAAGAAACTGGTAATCTGGT
1216823 CAGCTGAGTTGGAGACGGC-AAGATGTTTGGGTTTTTGATA-TGATGAGACTCTGTTGTCCAACC
1 CAGCTGAG-TGGAGACGGCAAAGA-GTTTGGGTTTTTGATATTGATGAGACTCTGTTGTCCAACC
1216886 TTCCTTACTACGTTGAGCATGGTTATGGGTAAGATTTTGATTTGGTCGTTTCCTTTTCTTCTCCA
64 TTCCTTACTACGTTGAGCATGGTTATGGGTAAGATTTTGATTTGGTCGTTTCCTTTTCTTCTCCA
1216951 ATTTTCTTGAACTTGTTTGGTTGCTAAGAAACTGGTAATCTGGT
129 ATTTTCTTGAACTTGTTTGGTTGCTAAGAAACTGGTAATCTGGT
1216995 GCAAAAAGTA
Statistics
Matches: 167, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
169 47 0.28
170 39 0.23
171 26 0.16
172 55 0.33
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (172 bp):
CAGCTGAGTGGAGACGGCAAAGAGTTTGGGTTTTTGATATTGATGAGACTCTGTTGTCCAACCTT
CCTTACTACGTTGAGCATGGTTATGGGTAAGATTTTGATTTGGTCGTTTCCTTTTCTTCTCCAAT
TTTCTTGAACTTGTTTGGTTGCTAAGAAACTGGTAATCTGGT
Found at i:1222915 original size:2 final size:2
Alignment explanation
Indices: 1222908--1222948 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1222898 TAGTTCTGCC
1222908 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1222949 GAGAGAGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1222968 original size:4 final size:4
Alignment explanation
Indices: 1222961--1223140 Score: 118
Period size: 4 Copynumber: 44.8 Consensus size: 4
1222951 GAGAGAGAGG
* *
1222961 GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGAGG GGGA GAGA GGGA
1 GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GG-GA GGGA GGGA GGGA
*
1223010 GAGG- GAGA GGGA -GGA GGGA GGGA GGGA -GG- GGGA GGGA GGGA GAGAGA
1 G-GGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA G-G-GA
* * * * * * * *
1223057 GGGA GAGA GAGA GAGA GAGA -GGA GGGA GAGA GGAGA GAGA GAGA GAGA
1 GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GG-GA GGGA GGGA GGGA
* * * * * *
1223105 GAGA GAGA GGGGA GAGA GAGA GGGA GAGA GAGA GGG
1 GGGA GGGA -GGGA GGGA GGGA GGGA GGGA GGGA GGG
1223141 GATAGAGAGA
Statistics
Matches: 149, Mismatches: 16, Indels: 22
0.80 0.09 0.12
Matches are distributed among these distances:
3 10 0.07
4 123 0.83
5 13 0.09
6 3 0.02
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (4 bp):
GGGA
Found at i:1222978 original size:12 final size:12
Alignment explanation
Indices: 1222955--1223187 Score: 171
Period size: 12 Copynumber: 19.8 Consensus size: 12
1222945 TATAGAGAGA
*
1222955 GAGAGGGGGAGG
1 GAGAGAGGGAGG
*
1222967 GAGGGAGGGAGG
1 GAGAGAGGGAGG
*
1222979 GAGGGAGGGAGG
1 GAGAGAGGGAGG
1222991 GAG-GA-GG-GG
1 GAGAGAGGGAGG
1223000 GAGAGAGGGAGAG
1 GAGAGAGGGAG-G
1223013 G-GAGAGGGA-G
1 GAGAGAGGGAGG
*
1223023 GAGGGAGGGAGG
1 GAGAGAGGGAGG
1223035 GAG-G-GGGAGG
1 GAGAGAGGGAGG
*
1223045 GAGGGAGAGAGAGG
1 GA--GAGAGGGAGG
* *
1223059 GAGAGAGAGAGA
1 GAGAGAGGGAGG
1223071 GAGAGA-GGAGG
1 GAGAGAGGGAGG
*
1223082 GAGAGA-GGAGA
1 GAGAGAGGGAGG
* *
1223093 GAGAGAGAGAGA
1 GAGAGAGGGAGG
*
1223105 GAGAGAGAG-GG
1 GAGAGAGGGAGG
*
1223116 GAGAGAGAGAGG
1 GAGAGAGGGAGG
*
1223128 GAGAGAGAGAGGG
1 GAGAGAGGGA-GG
* * *
1223141 GATAGAGAGAGA
1 GAGAGAGGGAGG
*
1223153 GAGAGAGGAGAGA
1 GAGAGAGG-GAGG
* *
1223166 GAGAGAGAGAGA
1 GAGAGAGGGAGG
1223178 GAGGAGAGGG
1 GA-GAGAGGG
1223188 GTTGTCCACT
Statistics
Matches: 190, Mismatches: 16, Indels: 29
0.81 0.07 0.12
Matches are distributed among these distances:
9 5 0.03
10 14 0.07
11 41 0.22
12 92 0.48
13 31 0.16
14 7 0.04
ACGTcount: A:0.36, C:0.00, G:0.63, T:0.00
Consensus pattern (12 bp):
GAGAGAGGGAGG
Found at i:1223056 original size:2 final size:2
Alignment explanation
Indices: 1223049--1223185 Score: 178
Period size: 2 Copynumber: 71.5 Consensus size: 2
1223039 GGGAGGGAGG
* *
1223049 GA GA GA GA GG GA GA GA GA GA GA GA GA GA G- GA GG GA GA GA G-
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* *
1223089 GA GA GA GA GA GA GA GA GA GA GA GA G- GG GA GA GA GA GA GG GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* *
1223130 GA GA GA GA G- GG GA TA GA GA GA GA GA GA GA G- GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1223170 GA GA GA GA GA G- GA GA G
1 GA GA GA GA GA GA GA GA G
1223186 GGGTTGTCCA
Statistics
Matches: 119, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
1 6 0.05
2 113 0.95
ACGTcount: A:0.44, C:0.00, G:0.55, T:0.01
Consensus pattern (2 bp):
GA
Found at i:1223151 original size:4 final size:4
Alignment explanation
Indices: 1223000--1223185 Score: 179
Period size: 4 Copynumber: 48.2 Consensus size: 4
1222990 GGAGGAGGGG
* * * * * * * * *
1223000 GAGA GAGG GAGA GGGA GAGG GAG- GAGG GAGG GAGG GAGG GGGA GGGA
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
* * *
1223047 GGGA GAGA GAGG GAGA GAGA GAGA GAGA GAG- GAGG GAGA GAG- GAGA
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
* *
1223093 GAGA GAGA GAGA GAGA GAGA G-GG GAGA GAGA GAGG GAGA GAGA GAG-
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
* *
1223139 GGGA TAGA GAGA GAGA GAGA G-GA GAGA GAGA GAGA GAGA GAG- GAGA
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
1223185 G
1 G
1223186 GGGTTGTCCA
Statistics
Matches: 156, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
3 19 0.12
4 137 0.88
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.01
Consensus pattern (4 bp):
GAGA
Found at i:1226434 original size:29 final size:29
Alignment explanation
Indices: 1226347--1226434 Score: 68
Period size: 29 Copynumber: 3.0 Consensus size: 29
1226337 TTTAGGGATT
* *
1226347 AAATTAAAATATTCAAAAGTTTAAAGATT
1 AAATTAAAATATTTAAAAGTTTAAAGATG
** * ** * **
1226376 AGTTTATAACAAAAGTAATAGTTTGGAGATG
1 AAATTA-AA-ATATTTAAAAGTTTAAAGATG
1226407 AAATTAAAATATTTAAAAGTTTAAAGAT
1 AAATTAAAATATTTAAAAGTTTAAAGAT
1226435 CATTTTAAAA
Statistics
Matches: 39, Mismatches: 18, Indels: 4
0.64 0.30 0.07
Matches are distributed among these distances:
29 18 0.46
30 4 0.10
31 17 0.44
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.34
Consensus pattern (29 bp):
AAATTAAAATATTTAAAAGTTTAAAGATG
Found at i:1229310 original size:3 final size:3
Alignment explanation
Indices: 1229302--1229346 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1229292 ACCCTATATT
1229302 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1229347 AAGCTAGCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1229919 original size:21 final size:21
Alignment explanation
Indices: 1229868--1229920 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
1229858 ATTATGACTA
1229868 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* *
1229889 TTG-AGTTGCGATTTTCCCAA-T
1 TCGCA-ATGCGATTTT-CCAATT
1229910 TCGCAATGCGA
1 TCGCAATGCGA
1229921 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
20 1 0.04
21 19 0.76
22 5 0.20
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1229935 original size:20 final size:21
Alignment explanation
Indices: 1229910--1229961 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1229900 TTTTCCCAAT
*
1229910 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
1229930 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1229951 TCGCAATGCGA
1 TCGCAATGCGA
1229962 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1229974 original size:41 final size:42
Alignment explanation
Indices: 1229929--1230064 Score: 145
Period size: 41 Copynumber: 3.3 Consensus size: 42
1229919 GAATAAGTAA
* ** *
1229929 ATCGCAATGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGATATTGACAAAATCGCAACGCGATACTGACT
*
1229970 ATCGCAACGCGATAAT-ACAAAATCGCAACGCGATACTGACT
1 ATCGCAACGCGATATTGACAAAATCGCAACGCGATACTGACT
* ** *
1230011 TTCGCAACGCGATATTGAC--TTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATATTGACAAAATCGCAACGCGATACTGACT
* *
1230051 TTCGCAACGAGATA
1 ATCGCAACGCGATA
1230065 ATACATAATC
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
40 31 0.38
41 47 0.57
42 4 0.05
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (42 bp):
ATCGCAACGCGATATTGACAAAATCGCAACGCGATACTGACT
Found at i:1229975 original size:20 final size:20
Alignment explanation
Indices: 1229950--1230064 Score: 124
Period size: 20 Copynumber: 5.7 Consensus size: 20
1229940 AATTGGGAAA
*
1229950 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1229970 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
1229991 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1230011 TTCGCAACGCGATATTGACT
1 ATCGCAACGCGATACTGACT
* *
1230031 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
1230051 TTCGCAACGAGATA
1 ATCGCAACGCGATA
1230065 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 62 0.77
21 15 0.19
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1230049 original size:40 final size:40
Alignment explanation
Indices: 1229948--1230084 Score: 159
Period size: 41 Copynumber: 3.4 Consensus size: 40
1229938 CGAATTGGGA
* *
1229948 AAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
1229988 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATATTGAC
1 -AAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** * *
1230030 -TTTCGCAACGCGATTCTGACTTTCGCAACGAGATAATAC
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
1230069 ATAATCACAATGCGAT
1 A-AATCGCAACGCGAT
1230085 TTTCAAAGCG
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 2 0.02
40 32 0.40
41 45 0.56
42 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (40 bp):
AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:1230584 original size:20 final size:20
Alignment explanation
Indices: 1230535--1230593 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1230525 TTTATTCTCT
* **
1230535 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
1230555 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
1230575 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
1230594 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:1230784 original size:25 final size:24
Alignment explanation
Indices: 1230730--1230784 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1230720 TGTTTATTAT
* *
1230730 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1230754 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1230780 TGTTT
1 TGTTT
1230785 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1231934 original size:21 final size:21
Alignment explanation
Indices: 1231908--1231965 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
1231898 ATTTTACACT
1231908 TAGGGAACCGATTCCCTATGA
1 TAGGGAACCGATTCCCTATGA
1231929 TAGGGAACCGATTCCCTATGA
1 TAGGGAACCGATTCCCTATGA
1231950 TAGGGAACCGATTCCC
1 TAGGGAACCGATTCCC
1231966 CCCACTGTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (21 bp):
TAGGGAACCGATTCCCTATGA
Found at i:1237671 original size:21 final size:22
Alignment explanation
Indices: 1237646--1237728 Score: 89
Period size: 21 Copynumber: 3.8 Consensus size: 22
1237636 TTGGTGCATA
*
1237646 GGGAATCGATTCCCCCCTTGA-
1 GGGAACCGATTCCCCCCTTGAG
*
1237667 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCTTG-AG
**
1237690 GGGAACCGATTCCCCCC-ACAG
1 GGGAACCGATTCCCCCCTTGAG
* *
1237711 GGGAATCGATACCCCCCT
1 GGGAACCGATTCCCCCCT
1237729 GGGGTTCTGC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
21 35 0.67
22 1 0.02
23 16 0.31
ACGTcount: A:0.22, C:0.36, G:0.24, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCTTGAG
Found at i:1241579 original size:18 final size:18
Alignment explanation
Indices: 1241558--1241605 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
1241548 TCCACTTCGG
*
1241558 GAGCCATCACCTTACCCA
1 GAGCCATCACCTCACCCA
* *
1241576 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
1241594 GAGCCATCACCT
1 GAGCCATCACCT
1241606 GATTTACCCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.27, C:0.42, G:0.12, T:0.19
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1242194 original size:19 final size:20
Alignment explanation
Indices: 1242140--1242206 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1242130 TAGTTTACTT
* *
1242140 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1242160 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1242180 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1242199 TCGCAACG
1 TCGCAACG
1242207 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1242254 original size:19 final size:19
Alignment explanation
Indices: 1242232--1242328 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
1242222 GAAACACAAA
1242232 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1242251 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
*
1242267 TCG--TTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1242284 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1242300 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1242317 TTGCATTGCGAT
1 TCGCATTGCGAT
1242329 AGCCATTTCC
Statistics
Matches: 60, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
14 11 0.18
15 6 0.10
16 8 0.13
17 7 0.12
18 6 0.10
19 22 0.37
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1242273 original size:14 final size:14
Alignment explanation
Indices: 1242254--1242312 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1242244 TTTCATTTCG
1242254 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
* *
1242268 CGTTGCAATTTTCATTT
1 CGTTGCGA-TTT--TGT
1242285 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1242301 CGTTGCGATTTT
1 CGTTGCGATTTT
1242313 CATTTTGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 17 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 5 0.14
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1242284 original size:33 final size:33
Alignment explanation
Indices: 1242237--1242328 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
1242227 ACAAATCGCA
*
1242237 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
1242270 TTGCAATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
1242303 TTGCGATTTTCATTTTGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1242329 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.13, C:0.17, G:0.21, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1242368 original size:40 final size:40
Alignment explanation
Indices: 1242322--1242407 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
1242312 TCATTTTGCA
* * * *
1242322 TTGCGATAGCCATTTCCGCGTTACGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCGTTACAAAAGTAAGTTTCGTG
* * *
1242362 TTGCGATAGTCATTTTCGCGTTGCAAAAGTAAGTTTCGTG
1 TTGCGATAGCCATTTCCGCGTTACAAAAGTAAGTTTCGTG
1242402 TTGCGA
1 TTGCGA
1242408 AAGTAAACTA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (40 bp):
TTGCGATAGCCATTTCCGCGTTACAAAAGTAAGTTTCGTG
Found at i:1242384 original size:20 final size:20
Alignment explanation
Indices: 1242301--1242385 Score: 100
Period size: 20 Copynumber: 4.3 Consensus size: 20
1242291 GCGATTTTGT
**
1242301 CGTTGCGATTTTCATTTT-G
1 CGTTGCGATAGTCATTTTCG
* * *
1242320 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTTTCG
*
1242340 CGTTACGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
1242360 TGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1242380 CGTTGC
1 CGTTGC
1242386 AAAAGTAAGT
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 13 0.25
20 40 0.75
ACGTcount: A:0.15, C:0.21, G:0.22, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1242398 original size:20 final size:20
Alignment explanation
Indices: 1242375--1242413 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1242365 CGATAGTCAT
1242375 TTTCGCGTTGCAAAAGTAAG
1 TTTCGCGTTGCAAAAGTAAG
* *
1242395 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCAAAAGTAA
1242414 ACTATTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (20 bp):
TTTCGCGTTGCAAAAGTAAG
Found at i:1242808 original size:21 final size:20
Alignment explanation
Indices: 1242756--1242816 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
1242746 GACTCACCTG
1242756 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGTCCCCT
* ** *
1242776 CCAATCGTTCAAGAGGCCCCT
1 TC-ATCCCTCAAGAGTCCCCT
1242797 ATCATCCCTCAAGAGTCCCC
1 -TCATCCCTCAAGAGTCCCC
1242817 CCGTTCAAGA
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.23, C:0.43, G:0.13, T:0.21
Consensus pattern (20 bp):
TCATCCCTCAAGAGTCCCCT
Found at i:1242839 original size:37 final size:40
Alignment explanation
Indices: 1242753--1242839 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 40
1242743 CCCGACTCAC
**
1242753 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCC-A-CGTTCAAGAGGCAA
*
1242795 CTATCATCCCTCAAGAGT-CCC-CC-CGTTCAAGAGGCAA
1 CTGTCATCCCTCAAGAGTCCCCTCCACGTTCAAGAGGCAA
1242832 CTGTCATC
1 CTGTCATC
1242840 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
37 19 0.46
40 2 0.05
41 3 0.07
42 17 0.41
ACGTcount: A:0.23, C:0.39, G:0.16, T:0.22
Consensus pattern (40 bp):
CTGTCATCCCTCAAGAGTCCCCTCCACGTTCAAGAGGCAA
Found at i:1244404 original size:20 final size:20
Alignment explanation
Indices: 1244375--1244412 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1244365 TGTTGAAGGT
*
1244375 AAAACAGACTGTCGCAACAC
1 AAAACAGACTATCGCAACAC
*
1244395 AAAACTGACTATCGCAAC
1 AAAACAGACTATCGCAAC
1244413 GAGAGAATCG
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:0.45, C:0.29, G:0.13, T:0.13
Consensus pattern (20 bp):
AAAACAGACTATCGCAACAC
Found at i:1244470 original size:19 final size:19
Alignment explanation
Indices: 1244418--1244463 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1244408 GCAACGAGAG
1244418 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1244437 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1244456 AATCGCAA
1 AATCGCAA
1244464 CGAGAAAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1244542 original size:19 final size:20
Alignment explanation
Indices: 1244502--1244575 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
1244492 CGCGTTGCGG
*
1244502 TTTTCTCGTTGCGATAGCCA
1 TTTTCGCGTTGCGATAGCCA
*
1244522 TTTTTGCGTTGCGAT-GCCA
1 TTTTCGCGTTGCGATAGCCA
*
1244541 TTTTCGCGTTGCGATAGTCA
1 TTTTCGCGTTGCGATAGCCA
1244561 TTTTCGCGTTGCGAT
1 TTTTCGCGTTGCGAT
1244576 TTCCTCGTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 18 0.37
20 31 0.63
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.42
Consensus pattern (20 bp):
TTTTCGCGTTGCGATAGCCA
Found at i:1244590 original size:34 final size:34
Alignment explanation
Indices: 1244489--1244594 Score: 122
Period size: 34 Copynumber: 3.0 Consensus size: 34
1244479 GCGATTTTCA
* *
1244489 TTTCGCGTTGCGGTTTTCTCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTCGTTGCGATAGTCAT
* *
1244523 TTTTGCGTTGCGATGCCATTTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGC---G--ATTTTCTCGTTGCGATAGTCAT
*
1244562 TTTCGCGTTGCGATTTCCTCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCTCGTTGCGATAGTCA
1244595 AATGAATGTC
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
34 29 0.48
36 1 0.02
37 1 0.02
39 29 0.48
ACGTcount: A:0.11, C:0.23, G:0.25, T:0.41
Consensus pattern (34 bp):
TTTCGCGTTGCGATTTTCTCGTTGCGATAGTCAT
Found at i:1244969 original size:20 final size:20
Alignment explanation
Indices: 1244944--1245004 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
1244934 ATGTCGATCT
*
1244944 CGTTGCGAAATTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
1244964 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
* *
1244984 CGTTGCGATAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
1245004 C
1 C
1245005 ATTGTGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:1245094 original size:21 final size:22
Alignment explanation
Indices: 1245042--1245094 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1245032 ATTTACTTAT
1245042 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
1245063 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
1245084 TCGCATTGCGA
1 TCGCATTGCGA
1245095 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:1250935 original size:21 final size:21
Alignment explanation
Indices: 1250909--1250963 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1250899 ATTCTGACTA
1250909 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
** * *
1250930 TCGCATTATGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
1250951 TCGCAATGCGATT
1 TCGCATTGCGATT
1250964 ACGTAAATCG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1250976 original size:20 final size:20
Alignment explanation
Indices: 1250951--1251003 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1250941 TTTTCCTAAT
1250951 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
*
1250971 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
1250991 TCGCAATGCGATT
1 TCGCAATGCGATT
1251004 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:1251234 original size:22 final size:22
Alignment explanation
Indices: 1251183--1251240 Score: 79
Period size: 18 Copynumber: 2.8 Consensus size: 22
1251173 ACATCCGTCC
1251183 CCATCTCCGACGAAATCAGTCT
1 CCATCTCCGACGAAATCAGTCT
*
1251205 CCA----CGACGATATCAGTCT
1 CCATCTCCGACGAAATCAGTCT
1251223 CCATCTCCGACGAAATCA
1 CCATCTCCGACGAAATCA
1251241 TTCACAGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
18 17 0.57
22 13 0.43
ACGTcount: A:0.29, C:0.36, G:0.14, T:0.21
Consensus pattern (22 bp):
CCATCTCCGACGAAATCAGTCT
Found at i:1251634 original size:20 final size:20
Alignment explanation
Indices: 1251590--1251654 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
1251580 ACGATTTTCA
*
1251590 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
1251610 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* * **
1251630 TTTCGTGTTACGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
1251650 TTTCG
1 TTTCG
1251655 TATTGCGATT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:1251655 original size:20 final size:20
Alignment explanation
Indices: 1251576--1251665 Score: 74
Period size: 20 Copynumber: 4.5 Consensus size: 20
1251566 GCGATTCTGT
*
1251576 CGTTACGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
** **
1251595 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
**
1251615 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
* *
1251635 TGTTACGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
**
1251655 TATTGCGATTT
1 CGTTGCGATTT
1251666 AAAGTTTCAG
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
19 11 0.19
20 47 0.81
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:1253616 original size:20 final size:20
Alignment explanation
Indices: 1253554--1253637 Score: 63
Period size: 20 Copynumber: 4.5 Consensus size: 20
1253544 AGAATAGTTT
* *
1253554 ACTATCGCTATGCGAAAATG
1 ACTATCGCAAGGCGAAAATG
*
1253574 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAAGGCGAAAATG
*
1253590 A--ATCGCAAGGTGAAAATG
1 ACTATCGCAAGGCGAAAATG
* **
1253608 ACTATCGCAATGCGAATTTG
1 ACTATCGCAAGGCGAAAATG
1253628 ACTATCGCAA
1 ACTATCGCAA
1253638 CGAAAGAATC
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
14 7 0.14
16 3 0.06
17 4 0.08
18 4 0.08
20 32 0.64
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.21
Consensus pattern (20 bp):
ACTATCGCAAGGCGAAAATG
Found at i:1253709 original size:20 final size:20
Alignment explanation
Indices: 1253684--1253857 Score: 142
Period size: 20 Copynumber: 9.3 Consensus size: 20
1253674 GATTCTCTCG
**
1253684 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1253704 TTGCGATAATCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1253724 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1253744 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1253764 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
**
1253778 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1253797 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
* * *
1253811 TTGTGATAGTCATTTTTGCG
1 TTGCGATAGTCATTTTCGCA
*
1253831 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1253851 TTGCGAT
1 TTGCGAT
1253858 TTTAAGTTTC
Statistics
Matches: 129, Mismatches: 11, Indels: 28
0.77 0.07 0.17
Matches are distributed among these distances:
14 13 0.10
16 12 0.09
17 6 0.05
18 4 0.03
19 7 0.05
20 87 0.67
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1253824 original size:33 final size:33
Alignment explanation
Indices: 1253744--1253825 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
1253734 CATTTTCGCA
* * * *
1253744 TTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCA-TTTCGCATTGCGATTCTCTCG
**
1253778 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCATTGCGATTCTCTCG
*
1253811 TTGTGATAGTCATTT
1 TTGCGATAGTCATTT
1253826 TTGCGTTGCG
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
33 29 0.74
34 10 0.26
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCATTGCGATTCTCTCG
Found at i:1254382 original size:18 final size:19
Alignment explanation
Indices: 1254343--1254384 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1254333 CTCACCTGTC
1254343 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
1254364 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
1254382 ATC
1 ATC
1254385 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:1254393 original size:21 final size:22
Alignment explanation
Indices: 1254369--1254429 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 22
1254359 CCCCTATCGT
1254369 TCAAGAGGCCCCTATCATCC-C
1 TCAAGAGGCCCCTATCATCCAC
* * *
1254390 TCAAGAGTCCCCTCTCA-CCAT
1 TCAAGAGGCCCCTATCATCCAC
* *
1254411 TCAAGAGGCCACTGTCATC
1 TCAAGAGGCCCCTATCATC
1254430 GTTGAAGATG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 2 0.06
21 29 0.91
22 1 0.03
ACGTcount: A:0.25, C:0.39, G:0.15, T:0.21
Consensus pattern (22 bp):
TCAAGAGGCCCCTATCATCCAC
Found at i:1254445 original size:42 final size:42
Alignment explanation
Indices: 1254368--1254459 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 42
1254358 TCCCCTATCG
* * *
1254368 TTCAAGAGGCCCCTATCATCCCTCAAGAGTCCCCTCTCACCA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGTCCCCTCCCAACA
* ** *
1254410 TTCAAGAGGCCACTGTCATCGTTGAAGATGT-CCCTCCCAACA
1 TTCAAGAGGCCACTATCATCCCTCAAGA-GTCCCCTCCCAACA
*
1254452 TTCTAGAG
1 TTCAAGAG
1254460 CCCGATTCAC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
42 39 0.95
43 2 0.05
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.24
Consensus pattern (42 bp):
TTCAAGAGGCCACTATCATCCCTCAAGAGTCCCCTCCCAACA
Found at i:1255818 original size:14 final size:14
Alignment explanation
Indices: 1255799--1255834 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1255789 ATTGTTTAAT
1255799 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1255813 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1255827 TGATTTGT
1 TGATTTGT
1255835 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1256032 original size:20 final size:20
Alignment explanation
Indices: 1256007--1256101 Score: 138
Period size: 20 Copynumber: 4.7 Consensus size: 20
1255997 GTGATTCTCT
1256007 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1256027 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
1256047 CGTTGCGATAGTTATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1256067 TGTTGCGATAGTCAATATT-CG
1 CGTTGCGATAGTC-AT-TTCCG
1256088 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
1256102 AATGAATGTC
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 49 0.73
21 16 0.24
22 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1256051 original size:40 final size:41
Alignment explanation
Indices: 1256007--1256101 Score: 156
Period size: 40 Copynumber: 2.3 Consensus size: 41
1255997 GTGATTCTCT
1256007 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCAAT-TCCG
1 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCAATATCCG
* * *
1256047 CGTTGCGATAGTTATTTCCGTGTTGCGATAGTCAATATTCG
1 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCAATATCCG
1256088 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
1256102 AATGAATGTC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 34 0.68
41 16 0.32
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (41 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCAATATCCG
Found at i:1256446 original size:20 final size:20
Alignment explanation
Indices: 1256423--1256509 Score: 104
Period size: 20 Copynumber: 4.3 Consensus size: 20
1256413 CAGAATCTCG
1256423 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
*
1256443 TTGCAATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
* ** *
1256463 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
1256484 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1256504 TTGCGA
1 TTGCGA
1256510 ATTAGGAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
19 1 0.02
20 38 0.69
21 16 0.29
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:1256493 original size:41 final size:40
Alignment explanation
Indices: 1256423--1256509 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 40
1256413 CAGAATCTCG
*
1256423 TTGCGATTTACAGATTCGCATTGCAATTTACGTATTCGCA
1 TTGCGATTTACAAATTCGCATTGCAATTTACGTATTCGCA
* * *
1256463 TTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCA
1 TTGCGA-TTTACAAATTCGCATTGCAATTTACGTATTCGCA
1256504 TTGCGA
1 TTGCGA
1256510 ATTAGGAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 6 0.14
41 36 0.86
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.38
Consensus pattern (40 bp):
TTGCGATTTACAAATTCGCATTGCAATTTACGTATTCGCA
Found at i:1256530 original size:21 final size:21
Alignment explanation
Indices: 1256506--1256551 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1256496 TATTCGCATT
1256506 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
1256527 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1256548 GCGA
1 GCGA
1256552 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1257737 original size:21 final size:21
Alignment explanation
Indices: 1257711--1257755 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1257701 CTCGAGTTGG
1257711 ACCTAGAAATTGTAGATCTGA
1 ACCTAGAAATTGTAGATCTGA
*
1257732 ACCTAGAAATTGTGGATCTGA
1 ACCTAGAAATTGTAGATCTGA
1257753 ACC
1 ACC
1257756 GACATGCACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (21 bp):
ACCTAGAAATTGTAGATCTGA
Found at i:1261597 original size:30 final size:31
Alignment explanation
Indices: 1261553--1261614 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
1261543 CAAATGGTCT
*
1261553 CCGATTATACGGTGTTGTTTTATTAAGTCCC
1 CCGATTATACGGTGTTGCTTTATTAAGTCCC
* * *
1261584 CCGA-TATAGGGTGTTGCTTTGTTGAGTCCC
1 CCGATTATACGGTGTTGCTTTATTAAGTCCC
1261614 C
1 C
1261615 GACTATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (31 bp):
CCGATTATACGGTGTTGCTTTATTAAGTCCC
Found at i:1262213 original size:10 final size:10
Alignment explanation
Indices: 1262185--1262231 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
1262175 AAGTTTGTTT
*
1262185 TTTGTGTTTG
1 TTTGTGTTCG
*
1262195 TGT-TGTTCG
1 TTTGTGTTCG
*
1262204 TTTATGTTCG
1 TTTGTGTTCG
1262214 TTTGTGTTCG
1 TTTGTGTTCG
1262224 TTTGTGTT
1 TTTGTGTT
1262232 TTATCATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
9 7 0.22
10 25 0.78
ACGTcount: A:0.02, C:0.06, G:0.28, T:0.64
Consensus pattern (10 bp):
TTTGTGTTCG
Found at i:1269959 original size:28 final size:29
Alignment explanation
Indices: 1269925--1270003 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 29
1269915 TTTTTTTATT
* * *
1269925 TAAATATTTAAAGTATTTTTTATT-AAGA
1 TAAATATCTAAAATATTTTTTATTCAAAA
*
1269953 TAAATATCTAAAATATTTTTTTTTCAAAA
1 TAAATATCTAAAATATTTTTTATTCAAAA
*
1269982 TAAATACCTAAAATATTTTTTA
1 TAAATATCTAAAATATTTTTTA
1270004 AATCAAAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 21 0.48
29 23 0.52
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (29 bp):
TAAATATCTAAAATATTTTTTATTCAAAA
Found at i:1270194 original size:29 final size:29
Alignment explanation
Indices: 1270107--1270203 Score: 81
Period size: 28 Copynumber: 3.4 Consensus size: 29
1270097 TGAAAATTTT
* * * *
1270107 AAATAA-TTTAAGTACCTGTTTTGACATA
1 AAATAATTTTAAATACATATTTTGACTTA
* * *
1270135 AAAT-ATTTTAGATACATATTTTAACTAA
1 AAATAATTTTAAATACATATTTTGACTTA
* *
1270163 AAATAATTTTAAATACTTATTTTGATTTA
1 AAATAATTTTAAATACATATTTTGACTTA
*
1270192 AAAAATATTTTA
1 AAATA-ATTTTA
1270204 CGTACTTAAA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
27 1 0.02
28 23 0.43
29 23 0.43
30 6 0.11
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (29 bp):
AAATAATTTTAAATACATATTTTGACTTA
Found at i:1270202 original size:30 final size:28
Alignment explanation
Indices: 1270134--1270203 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
1270124 GTTTTGACAT
*
1270134 AAAATATTTTAGATACATATTTTAACTA
1 AAAATATTTTAAATACATATTTTAACTA
* **
1270162 AAAATAATTTTAAATACTTATTTTGATTTAA
1 AAAAT-ATTTTAAATACATATTTT-AACT-A
1270193 AAAATATTTTA
1 AAAATATTTTA
1270204 CGTACTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 5 0.14
29 16 0.46
30 8 0.23
31 6 0.17
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (28 bp):
AAAATATTTTAAATACATATTTTAACTA
Found at i:1270516 original size:27 final size:27
Alignment explanation
Indices: 1270478--1270534 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
1270468 AAAACATTAT
* *
1270478 TAAAATTAATAAAACGT-ATAATAATAA
1 TAAAATAAATAAAA-ATAATAATAATAA
1270505 TAAAATAAATAAAAATAATAATAATAA
1 TAAAATAAATAAAAATAATAATAATAA
1270532 TAA
1 TAA
1270535 TTTTAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (27 bp):
TAAAATAAATAAAAATAATAATAATAA
Found at i:1270544 original size:3 final size:3
Alignment explanation
Indices: 1270495--1270535 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
1270485 AATAAAACGT
*
1270495 ATA ATA ATA ATA A-A ATAA ATA AAA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA AT
1270536 TTTAATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1277011 original size:27 final size:28
Alignment explanation
Indices: 1276954--1277017 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 28
1276944 AATAATGTAT
* *
1276954 TTATAATTATTTATTATATTTTAAACGA
1 TTATAATAATTTATTATATTTTAAACAA
* *
1276982 TTATAATAATTT-TTATATTTTTAATAA
1 TTATAATAATTTATTATATTTTAAACAA
1277009 TTA-AATAAT
1 TTATAATAAT
1277018 ATACTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 6 0.19
27 15 0.47
28 11 0.34
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (28 bp):
TTATAATAATTTATTATATTTTAAACAA
Found at i:1279195 original size:15 final size:15
Alignment explanation
Indices: 1279175--1279203 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1279165 ATATATCTCT
1279175 TCTCATTTACATTTA
1 TCTCATTTACATTTA
1279190 TCTCATTTACATTT
1 TCTCATTTACATTT
1279204 CTAAGCCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTCATTTACATTTA
Found at i:1287223 original size:31 final size:31
Alignment explanation
Indices: 1287188--1287250 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
1287178 AATTCGGTGA
1287188 ATTCAATATGTCCTTCTCACTAGGAACTCCC
1 ATTCAATATGTCCTTCTCACTAGGAACTCCC
*
1287219 ATTCAATATGTCCTTCTCATTAGGAACTCCC
1 ATTCAATATGTCCTTCTCACTAGGAACTCCC
1287250 A
1 A
1287251 AACTCTTGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (31 bp):
ATTCAATATGTCCTTCTCACTAGGAACTCCC
Found at i:1293772 original size:2 final size:2
Alignment explanation
Indices: 1293765--1293792 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1293755 TTATTTCAAA
1293765 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
1293793 TAAATTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1294041 original size:61 final size:61
Alignment explanation
Indices: 1293926--1294042 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 61
1293916 AGCTTAGGTT
* **
1293926 GAGTTTCAATTTTTTATTTAAAGTTCGAGTCGAGCTTAAAAATTTTAAGTTTGTGAGAGTG
1 GAGTTTCAATTTTTTATTTAAAGTTCGAGTCGAACTTAAAAATTTTAAACTTGTGAGAGTG
* * * * *
1293987 GAGTTTTAATTTTTTATTTCGAA-TTCGAGTTGAACTTGATAATTTTAAACTTGTGA
1 GAGTTTCAATTTTTTATTT-AAAGTTCGAGTCGAACTTAAAAATTTTAAACTTGTGA
1294043 ACTTTTAAGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
61 45 0.96
62 2 0.04
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.45
Consensus pattern (61 bp):
GAGTTTCAATTTTTTATTTAAAGTTCGAGTCGAACTTAAAAATTTTAAACTTGTGAGAGTG
Found at i:1295870 original size:6 final size:6
Alignment explanation
Indices: 1295859--1295896 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
1295849 AAATTGAACA
*
1295859 TGGTTC TGGTTC TGGTTC TGGCTC TGGTTC TGGTTC TG
1 TGGTTC TGGTTC TGGTTC TGGTTC TGGTTC TGGTTC TG
1295897 CTACCAGTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.18, G:0.34, T:0.47
Consensus pattern (6 bp):
TGGTTC
Found at i:1302529 original size:31 final size:30
Alignment explanation
Indices: 1302472--1302594 Score: 106
Period size: 31 Copynumber: 4.1 Consensus size: 30
1302462 TTATTAAAAC
* * *
1302472 TTTT-AAAA-ATTATTAAATAATCATTAAG
1 TTTTAAAAATATTATAAAATAATAATTAAA
1302500 TTTTAAAAATATTCATAAAATAATAATTAAA
1 TTTTAAAAATATT-ATAAAATAATAATTAAA
* * * * *
1302531 TTTGATCAATTATTATAAAATGATTATTAAA
1 TTTTA-AAAATATTATAAAATAATAATTAAA
* * *
1302562 TTTATAAAAATATTACAAAATTATCATTAAA
1 TTT-TAAAAATATTATAAAATAATAATTAAA
1302593 TT
1 TT
1302595 ATTTTTTGAC
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
28 4 0.05
29 4 0.05
30 3 0.04
31 58 0.76
32 7 0.09
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (30 bp):
TTTTAAAAATATTATAAAATAATAATTAAA
Found at i:1303533 original size:27 final size:25
Alignment explanation
Indices: 1303499--1303583 Score: 82
Period size: 27 Copynumber: 3.2 Consensus size: 25
1303489 AGAAAGCAAA
1303499 AATAAAATAGTAAGTAAACAAAAAAAT
1 AATAAAATA-TAA-TAAACAAAAAAAT
*
1303526 AATAAAATATATATAAAAAAAAGAAAAT
1 AATAAAATATA-AT-AAACAAA-AAAAT
* *
1303554 AAATAAAACA-AATAAACAAAATAAT
1 -AATAAAATATAATAAACAAAAAAAT
1303579 AATAA
1 AATAA
1303584 CAAAGTACGA
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
24 5 0.10
25 4 0.08
26 9 0.18
27 18 0.36
28 6 0.12
29 8 0.16
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.19
Consensus pattern (25 bp):
AATAAAATATAATAAACAAAAAAAT
Found at i:1303925 original size:2 final size:2
Alignment explanation
Indices: 1303880--1303906 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1303870 CTTGTGTAGA
1303880 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
1303907 ATAGTAAAAT
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:1304154 original size:12 final size:11
Alignment explanation
Indices: 1304126--1304166 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
1304116 TAACAAAATA
* *
1304126 AATAATATAAA
1 AATAATACAAG
1304137 AATAATACAAG
1 AATAATACAAG
1304148 TAATAATACAAG
1 -AATAATACAAG
1304160 AATAATA
1 AATAATA
1304167 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Done.