Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold222
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: 1154749
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.31
Warning! 71027 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:958311 original size:20 final size:20
Alignment explanation
Indices: 958232--958322 Score: 80
Period size: 20 Copynumber: 4.5 Consensus size: 20
958222 TGCTAACAAA
*
958232 AGCACAAATGTGCTATCAGG
1 AGCACGAATGTGCTATCAGG
* * *
958252 AGCACCGTA-GTGTTATCAGA
1 AGCA-CGAATGTGCTATCAGG
958272 AGCACCGTAA--TGCTATCAGG
1 AGCA-CG-AATGTGCTATCAGG
958292 AGCACGAATGTGCTATCAGG
1 AGCACGAATGTGCTATCAGG
* *
958312 GGTACGAATGT
1 AGCACGAATGT
958323 ATTATCAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
18 2 0.03
19 2 0.03
20 51 0.88
21 3 0.05
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (20 bp):
AGCACGAATGTGCTATCAGG
Found at i:958328 original size:60 final size:60
Alignment explanation
Indices: 958205--958336 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 60
958195 ATGATTATGC
* * * *
958205 TATCAGAGGCACCGTAGTGCTAACAAAAGCACAAATGTGCTATCAGGAGCACCGTAGTGT
1 TATCAGAAGCACCGTAATGCTAACAAAAGCACAAATGTGCTATCAGGAGCACCGAAGTAT
* ** * * *
958265 TATCAGAAGCACCGTAATGCTATCAGGAGCACGAATGTGCTATCAGGGGTA-CGAATGTAT
1 TATCAGAAGCACCGTAATGCTAACAAAAGCACAAATGTGCTATCAGGAGCACCGAA-GTAT
*
958325 TATCAAAAGCAC
1 TATCAGAAGCAC
958337 TTTTTCAAGA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 3 0.05
60 57 0.95
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.21
Consensus pattern (60 bp):
TATCAGAAGCACCGTAATGCTAACAAAAGCACAAATGTGCTATCAGGAGCACCGAAGTAT
Found at i:963298 original size:28 final size:28
Alignment explanation
Indices: 963262--963317 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
963252 TGCAGGTTGG
*
963262 TTCAGACATGGAAATCGACAAGCAAGGT
1 TTCAGACATGGAAATCGAAAAGCAAGGT
963290 TTCAGACATGGAAATCGAAAAGCAAGGT
1 TTCAGACATGGAAATCGAAAAGCAAGGT
963318 ACTGAGTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.18
Consensus pattern (28 bp):
TTCAGACATGGAAATCGAAAAGCAAGGT
Found at i:965037 original size:39 final size:42
Alignment explanation
Indices: 964992--965092 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 42
964982 TTTCCTTATG
964992 CTATTACGCCTCTATTC-T-ATTCAACCAAACACA-AGAA-TA
1 CTATTACGCCTCTATTCATAATTCAACCAAACA-ATAGAATTA
* *
965031 CTATTACGCCTCTATTCCATTACATTCAACCAAACAATTGAATTG
1 CTATTACGCCTCTATT-CA-TA-ATTCAACCAAACAATAGAATTA
965076 CTATTACGCCTCTATTC
1 CTATTACGCCTCTATTC
965093 CGTTACGCCT
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
39 16 0.30
40 1 0.02
42 1 0.02
43 1 0.02
44 17 0.32
45 17 0.32
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.33
Consensus pattern (42 bp):
CTATTACGCCTCTATTCATAATTCAACCAAACAATAGAATTA
Found at i:965100 original size:16 final size:16
Alignment explanation
Indices: 965078--965114 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
965068 TTGAATTGCT
965078 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
965094 GTTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
965110 ATTAC
1 ATTAC
965115 AGTAAACCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.19, C:0.35, G:0.08, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:971423 original size:3 final size:3
Alignment explanation
Indices: 971415--971471 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
971405 ATGTTTTTAT
971415 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
971462 ATA ATA ATA A
1 ATA ATA ATA A
971472 AGTCTTTTCA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:979205 original size:25 final size:25
Alignment explanation
Indices: 979169--979221 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
979159 TTACCGACAT
* *
979169 CATGCTACTGCCTTCATTGTCGCAA
1 CATGCTACTGCCCTCAATGTCGCAA
* *
979194 CATGCTATTGCCCTCAATGTCGCGA
1 CATGCTACTGCCCTCAATGTCGCAA
979219 CAT
1 CAT
979222 TCATCCTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.21, C:0.32, G:0.17, T:0.30
Consensus pattern (25 bp):
CATGCTACTGCCCTCAATGTCGCAA
Found at i:979634 original size:20 final size:21
Alignment explanation
Indices: 979593--979642 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
979583 ATTTAGTTTA
*
979593 TTATATTATTATTTTCTTATT
1 TTATATTATTATTATCTTATT
*
979614 TTGTATTATTATTAT-TTATT
1 TTATATTATTATTATCTTATT
979634 TTATATTAT
1 TTATATTAT
979643 ATCTACAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (21 bp):
TTATATTATTATTATCTTATT
Found at i:981809 original size:41 final size:42
Alignment explanation
Indices: 981744--981829 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 42
981734 AGCATAAACA
* *
981744 GTGAGTTACACGGCCTGGACACACGTCCGTGTCCCTG-CCGT
1 GTGACTTACACGGCCTGGACACACGCCCGTGTCCCTGACCGT
** *
981785 GTGACTTACACGGCCTGGGTACACGCCCGTGTCTCTGACCGT
1 GTGACTTACACGGCCTGGACACACGCCCGTGTCCCTGACCGT
981827 GTG
1 GTG
981830 GTTTTATACC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 32 0.82
42 7 0.18
ACGTcount: A:0.14, C:0.33, G:0.30, T:0.23
Consensus pattern (42 bp):
GTGACTTACACGGCCTGGACACACGCCCGTGTCCCTGACCGT
Found at i:995103 original size:121 final size:122
Alignment explanation
Indices: 994962--995205 Score: 465
Period size: 121 Copynumber: 2.0 Consensus size: 122
994952 TAAAGTTTGG
994962 ATATTGACTAATTTTAATTTACCAAATTATATATTAAAAAATTGAAAATTTTGATTTAATTTTTA
1 ATATTGACTAATTTTAATTTACCAAATTATATATTAAAAAATTGAAAATTTTGATTTAATTTTTA
995027 TTCTTTTATTTTGCTTTAAGAAAAA-TAAATTAAAATTATTAAAATATATATTACCTA
66 TTCTTTTATTTTGCTTTAAGAAAAATTAAA-TAAAATTATTAAAATATATATTACCTA
995084 ATATTGACT-ATTTTAATTTACCAAATTATATATTAAAAAATTGAAAATTTTGATTTAATTTTTA
1 ATATTGACTAATTTTAATTTACCAAATTATATATTAAAAAATTGAAAATTTTGATTTAATTTTTA
995148 TTCTTTTATTTTGCTTTAAGAAAAATTAAATAAAATTATTAAAATATATATTACCTA
66 TTCTTTTATTTTGCTTTAAGAAAAATTAAATAAAATTATTAAAATATATATTACCTA
995205 A
1 A
995206 GGAAGCTGTT
Statistics
Matches: 121, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
121 108 0.89
122 13 0.11
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (122 bp):
ATATTGACTAATTTTAATTTACCAAATTATATATTAAAAAATTGAAAATTTTGATTTAATTTTTA
TTCTTTTATTTTGCTTTAAGAAAAATTAAATAAAATTATTAAAATATATATTACCTA
Found at i:997940 original size:16 final size:16
Alignment explanation
Indices: 997919--997958 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
997909 TTGAATTACT
997919 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
997935 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
997951 ATTACAGC
1 ATTACAGC
997959 GAACCAAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.33, G:0.05, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:1008220 original size:40 final size:39
Alignment explanation
Indices: 1008174--1008313 Score: 147
Period size: 40 Copynumber: 3.5 Consensus size: 39
1008164 GCGTTTGGAC
*
1008174 AAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTT
1 AAAAAACGCCGCTAAAAATCGAGCATTAGCGACGCTTTT
* *
1008213 CATAAAACGCCGCTAAAGATCGAGCATTAGCGACGCTTTT
1 -AAAAAACGCCGCTAAAAATCGAGCATTAGCGACGCTTTT
* * * * * *
1008253 AGGAAAGCGCCACTAAAAAT-GAGAATTAGCGCCGTTTTTT
1 A-AAAAACGCCGCTAAAAATCGAGCATTAGCGACG-CTTTT
*
1008293 GAAAAAACGCCGCAAAAAATC
1 -AAAAAACGCCGCTAAAAATC
1008314 TAAGCCCAAC
Statistics
Matches: 82, Mismatches: 14, Indels: 7
0.80 0.14 0.07
Matches are distributed among these distances:
39 13 0.16
40 68 0.83
41 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (39 bp):
AAAAAACGCCGCTAAAAATCGAGCATTAGCGACGCTTTT
Found at i:1008446 original size:40 final size:40
Alignment explanation
Indices: 1008346--1008521 Score: 203
Period size: 41 Copynumber: 4.3 Consensus size: 40
1008336 TGACCTTTTG
* * *
1008346 GGGCTTTAGTGGC-ATTTTTGAAAAATCGCCGCTAATGCTC
1 GGGCTTTAGCGGCGCTTTTTCAAAAA-CGCCGCTAATGCTC
** * *
1008386 AAGCTTTTAGCGACGCTTTTTCAAAAACGTCGCTAATGCTC
1 GGGC-TTTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTC
1008427 GGGCTTTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTC
1 GGGCTTTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTC
* **
1008467 GGGCCTTTAGCGGCG-TTTTCCAAGAAGTGCCGCTAATGCTC
1 GGG-CTTTAGCGGCGCTTTTTCAA-AAACGCCGCTAATGCTC
1008508 AGGGCTTTAGCGGC
1 -GGGCTTTAGCGGC
1008522 ATTTTGAAAA
Statistics
Matches: 117, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
40 46 0.39
41 58 0.50
42 13 0.11
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (40 bp):
GGGCTTTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTC
Found at i:1008501 original size:81 final size:82
Alignment explanation
Indices: 1008346--1008526 Score: 226
Period size: 81 Copynumber: 2.2 Consensus size: 82
1008336 TGACCTTTTG
* * * *
1008346 GGGCTTTAGTGGCATTTTTGAAAAATCGCCGCTAATGCTCAAGCTTTTAGCGACGCTTTTTCAAA
1 GGGCTTTAGCGGCATTTTTCAAAAATCGCCGCTAATGCTCAAGCCTTTAGCGACGCTTTTCCAAA
1008411 AACGTCGCTAATGCTC-
66 AACGTCGCTAATGCTCA
* ** *
1008427 GGGCTTTAGCGGCGCTTTTTCAAAAA-CGCCGCTAATGCTCGGGCCTTTAGCGGCG-TTTTCCAA
1 GGGCTTTAGCGGC-ATTTTTCAAAAATCGCCGCTAATGCTCAAGCCTTTAGCGACGCTTTTCCAA
*
1008490 GAA-GTGCCGCTAATGCTCA
65 AAACGT--CGCTAATGCTCA
1008509 GGGCTTTAGCGGCATTTT
1 GGGCTTTAGCGGCATTTT
1008527 GAAAAAGTGC
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
79 2 0.02
80 9 0.10
81 52 0.60
82 23 0.27
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.30
Consensus pattern (82 bp):
GGGCTTTAGCGGCATTTTTCAAAAATCGCCGCTAATGCTCAAGCCTTTAGCGACGCTTTTCCAAA
AACGTCGCTAATGCTCA
Found at i:1008520 original size:41 final size:41
Alignment explanation
Indices: 1008346--1008539 Score: 188
Period size: 40 Copynumber: 4.8 Consensus size: 41
1008336 TGACCTTTTG
* * *
1008346 GGGCTTTAGTGGC-ATTTTTGAAAAA-TCGCCGCTAATGCTC
1 GGGCTTTAGCGGCGCTTTTTCAAAAAGT-GCCGCTAATGCTC
** *
1008386 AAGCTTTTAGCGACGCTTTTTCAAAAACGT--CGCTAATGCTC
1 GGGC-TTTAGCGGCGCTTTTTCAAAAA-GTGCCGCTAATGCTC
*
1008427 GGGCTTTAGCGGCGCTTTTTCAAAAA-CGCCGCTAATGCTC
1 GGGCTTTAGCGGCGCTTTTTCAAAAAGTGCCGCTAATGCTC
* *
1008467 GGGCCTTTAGCGGCG-TTTTCCAAGAAGTGCCGCTAATGCTC
1 GGG-CTTTAGCGGCGCTTTTTCAAAAAGTGCCGCTAATGCTC
* *
1008508 AGGGCTTTAGC-G-GCATTTTGAAAAAGTGCCGC
1 -GGGCTTTAGCGGCGCTTTTTCAAAAAGTGCCGC
1008540 AAAAATATTT
Statistics
Matches: 127, Mismatches: 17, Indels: 20
0.77 0.10 0.12
Matches are distributed among these distances:
39 1 0.01
40 61 0.48
41 51 0.40
42 13 0.10
44 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (41 bp):
GGGCTTTAGCGGCGCTTTTTCAAAAAGTGCCGCTAATGCTC
Found at i:1013441 original size:42 final size:42
Alignment explanation
Indices: 1013377--1013610 Score: 319
Period size: 42 Copynumber: 5.5 Consensus size: 42
1013367 TCTTGGCGTT
* * * *
1013377 TAAAGGTCTTGGTTTTTTGCGGCATTTGTGGGAAAAGCGCCAC
1 TAAAGGTCTTGGTCTTTAGCGGCATTT-TGGGTAAAGCGCCGC
*
1013420 TAAA-GTC-TGGTTCTTTAGCGGCGTTTTTGGGTAAAGCGCCGC
1 TAAAGGTCTTGG-TCTTTAGCGGC-ATTTTGGGTAAAGCGCCGC
* * *
1013462 TAAAGATCTTGGTCTTTAGCGGCGTTTTTGGTAAAGCGCCGC
1 TAAAGGTCTTGGTCTTTAGCGGCATTTTGGGTAAAGCGCCGC
*
1013504 TAAAGGTCTTGGTCTTTAGCGGCATTTTTGGTAAAGCGCCGC
1 TAAAGGTCTTGGTCTTTAGCGGCATTTTGGGTAAAGCGCCGC
* * *
1013546 TAAAGGTCTTGGTCTTTAACGACATTTTTGGTAAAGCGCCGC
1 TAAAGGTCTTGGTCTTTAGCGGCATTTTGGGTAAAGCGCCGC
1013588 TAAAGGTCTTGGTCTTTAGCGGC
1 TAAAGGTCTTGGTCTTTAGCGGC
1013611 GTTTGTGTGA
Statistics
Matches: 173, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
41 3 0.02
42 147 0.85
43 20 0.12
44 3 0.02
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (42 bp):
TAAAGGTCTTGGTCTTTAGCGGCATTTTGGGTAAAGCGCCGC
Found at i:1017888 original size:31 final size:31
Alignment explanation
Indices: 1017848--1017948 Score: 130
Period size: 31 Copynumber: 3.3 Consensus size: 31
1017838 GGCATCAATA
* * *
1017848 ATTCATATTTACATATTCATACCCTATAATC
1 ATTCATATTTGCATATTCATACCTTGTAATC
* * *
1017879 ATTCGTATTTGCATATTCACATCTTGTAATC
1 ATTCATATTTGCATATTCATACCTTGTAATC
* *
1017910 ATTCATATTTGCATTTTTATACCTTGTAATC
1 ATTCATATTTGCATATTCATACCTTGTAATC
1017941 ATTCATAT
1 ATTCATAT
1017949 AAATTTTCGG
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.47
Consensus pattern (31 bp):
ATTCATATTTGCATATTCATACCTTGTAATC
Found at i:1020902 original size:7 final size:7
Alignment explanation
Indices: 1020885--1020914 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
1020875 ATTTTTAAAC
1020885 ATAATTAT
1 ATAA-TAT
1020893 ATAATAT
1 ATAATAT
1020900 ATAATAT
1 ATAATAT
1020907 ATAATAT
1 ATAATAT
1020914 A
1 A
1020915 CAAATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATAATAT
Found at i:1029948 original size:7 final size:7
Alignment explanation
Indices: 1029938--1030052 Score: 53
Period size: 7 Copynumber: 16.7 Consensus size: 7
1029928 ATCTAGAATT
1029938 TTGAACC
1 TTGAACC
1029945 TTGAACC
1 TTGAACC
1029952 TTGAACC
1 TTGAACC
* *
1029959 TTAAACT
1 TTGAACC
1029966 TTGAA-C
1 TTGAACC
** *
1029972 TCAAATC
1 TTGAACC
*
1029979 TTGAACA
1 TTGAACC
1029986 TTGAA--
1 TTGAACC
*
1029991 TTCCAGACC
1 TT-GA-ACC
*
1030000 TCGAACC
1 TTGAACC
* *
1030007 TTAAACT
1 TTGAACC
1030014 TTGAACC
1 TTGAACC
1030021 TTGAA-C
1 TTGAACC
1030027 TCTGAA--
1 T-TGAACC
1030033 TTCGAACC
1 TT-GAACC
*
1030041 TTAAACC
1 TTGAACC
1030048 TTGAA
1 TTGAA
1030053 ACCCAATTTT
Statistics
Matches: 79, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
5 3 0.04
6 10 0.13
7 62 0.78
8 3 0.04
9 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.30
Consensus pattern (7 bp):
TTGAACC
Found at i:1037542 original size:20 final size:18
Alignment explanation
Indices: 1037511--1037547 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
1037501 AAGCAAACAT
1037511 AAAAAAATAAAACTAAAG
1 AAAAAAATAAAACTAAAG
1037529 AAAAAAATTGAAAACTAAA
1 AAAAAAA-T-AAAACTAAA
1037548 TTTAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (18 bp):
AAAAAAATAAAACTAAAG
Found at i:1038875 original size:11 final size:11
Alignment explanation
Indices: 1038861--1038903 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
1038851 ATTTTTTAAA
1038861 TTTTAAAATAT
1 TTTTAAAATAT
1038872 TTTTAAAATACTT
1 TTTTAAAATA--T
* *
1038885 TTTTTAAATTT
1 TTTTAAAATAT
1038896 TTTTAAAA
1 TTTTAAAA
1038904 AATTGGTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 18 0.67
13 9 0.33
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:1039636 original size:6 final size:6
Alignment explanation
Indices: 1039627--1039660 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
1039617 CAATGGGACG
1039627 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGGA
1 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGGA
1039661 TGGTGGGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:1046220 original size:9 final size:9
Alignment explanation
Indices: 1046206--1046241 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
1046196 NNNNNNNNNN
1046206 ATTCGAATT
1 ATTCGAATT
1046215 ATTCGAATT
1 ATTCGAATT
*
1046224 ATTCGAGTT
1 ATTCGAATT
1046233 ATTCGAATT
1 ATTCGAATT
1046242 TGAAAACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (9 bp):
ATTCGAATT
Found at i:1046311 original size:9 final size:9
Alignment explanation
Indices: 1046294--1046324 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1046284 TCGAGTTGAT
1046294 TCGAATAAC
1 TCGAATAAC
*
1046303 TCGATTAAC
1 TCGAATAAC
1046312 TCGAATAAC
1 TCGAATAAC
1046321 TCGA
1 TCGA
1046325 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:1046519 original size:18 final size:19
Alignment explanation
Indices: 1046493--1046529 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1046483 TTGTGGGTGT
1046493 TTTAAAAATT-TTATTTTA
1 TTTAAAAATTATTATTTTA
*
1046511 TTTATAAATTATTATTTTA
1 TTTAAAAATTATTATTTTA
1046530 ATAAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTAAAAATTATTATTTTA
Found at i:1051444 original size:22 final size:22
Alignment explanation
Indices: 1051419--1051496 Score: 122
Period size: 22 Copynumber: 3.5 Consensus size: 22
1051409 TGCACTAATG
*
1051419 AACAGAGAGCAC-TAAAGTGCTA
1 AACAGAGAGCACAT-ATGTGCTA
1051441 AACAGAGAGCACATATGTGCTA
1 AACAGAGAGCACATATGTGCTA
1051463 AACAGAGAGCACATATGTGCTA
1 AACAGAGAGCACATATGTGCTA
*
1051485 AACGGAGAGCAC
1 AACAGAGAGCAC
1051497 TGTCGTGTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
22 52 0.98
23 1 0.02
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.14
Consensus pattern (22 bp):
AACAGAGAGCACATATGTGCTA
Found at i:1051522 original size:25 final size:25
Alignment explanation
Indices: 1051413--1051543 Score: 79
Period size: 22 Copynumber: 5.6 Consensus size: 25
1051403 TTATTATGCA
*
1051413 CTAATGAA-CAGAGAGCACTAAAGTG
1 CTAAT-AATCAGAGAGCACTAACGTG
*
1051438 CT-A-AA-CAGAGAGCAC-ATATGTG
1 CTAATAATCAGAGAGCACTA-ACGTG
*
1051460 CT-A-AA-CAGAGAGCAC-ATATGTG
1 CTAATAATCAGAGAGCACTA-ACGTG
* **
1051482 CT-A-AA-CGGAGAGCACTGTCGTG
1 CTAATAATCAGAGAGCACTAACGTG
* *
1051504 TTAGTAATCAGAGAGCACTAACGTG
1 CTAATAATCAGAGAGCACTAACGTG
1051529 CTAATAATCAGAGAG
1 CTAATAATCAGAGAG
1051544 TGCTAAAGTT
Statistics
Matches: 89, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.01
22 56 0.63
24 3 0.03
25 29 0.33
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (25 bp):
CTAATAATCAGAGAGCACTAACGTG
Found at i:1052045 original size:8 final size:8
Alignment explanation
Indices: 1052032--1052059 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1052022 TGTTTTATAT
1052032 ATATAATA
1 ATATAATA
1052040 ATATAATA
1 ATATAATA
1052048 ATATAATA
1 ATATAATA
1052056 ATAT
1 ATAT
1052060 TTTAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:1056527 original size:41 final size:41
Alignment explanation
Indices: 1056458--1056575 Score: 145
Period size: 41 Copynumber: 3.0 Consensus size: 41
1056448 AAGGACGCCA
* *
1056458 CAAAAGGCTAG-ACTATAGCGGCATTTTTCTCATAAATGCTG
1 CAAAAGGTTAGAACTATAGCGGC-GTTTTCTCATAAATGCTG
* *
1056499 CAAAAGGTTAGAACTATAGCGGCGTTTTCTCACAAACGCTG
1 CAAAAGGTTAGAACTATAGCGGCGTTTTCTCATAAATGCTG
* *
1056540 CAAAAGGTAAGAA--ATAACGGCGTTTT-TCATAAATGC
1 CAAAAGGTTAGAACTATAGCGGCGTTTTCTCATAAATGC
1056576 CACGAATATT
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
38 8 0.12
39 12 0.18
41 37 0.54
42 11 0.16
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (41 bp):
CAAAAGGTTAGAACTATAGCGGCGTTTTCTCATAAATGCTG
Found at i:1058266 original size:43 final size:43
Alignment explanation
Indices: 1058218--1058334 Score: 153
Period size: 43 Copynumber: 2.7 Consensus size: 43
1058208 CAAGCCCGTG
* * *
1058218 TGGCTCACATGGCCAAGAGACACACCTGTGTGGTCAGGACGTA
1 TGGCTCACACGACCAAGAGACACGCCTGTGTGGTCAGGACGTA
* * * * * *
1058261 TGGCTCACACAACCAAGAGATATGCCCGTGTGGTCAGGCCGTG
1 TGGCTCACACGACCAAGAGACACGCCTGTGTGGTCAGGACGTA
1058304 TGGCTCACACGACCAAGAGACACGCCTGTGT
1 TGGCTCACACGACCAAGAGACACGCCTGTGT
1058335 CTCAGGCCGT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.25, C:0.28, G:0.29, T:0.18
Consensus pattern (43 bp):
TGGCTCACACGACCAAGAGACACGCCTGTGTGGTCAGGACGTA
Found at i:1059776 original size:23 final size:23
Alignment explanation
Indices: 1059732--1059779 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1059722 GGATAGCCAT
* * *
1059732 ATATCGGGAAGTTCAAGCGAGCC
1 ATATCGGAAAGCTCAAGAGAGCC
*
1059755 ATATCGGAAAGCTCTAGAGAGCC
1 ATATCGGAAAGCTCAAGAGAGCC
1059778 AT
1 AT
1059780 TAATCAGGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (23 bp):
ATATCGGAAAGCTCAAGAGAGCC
Found at i:1063916 original size:23 final size:23
Alignment explanation
Indices: 1063890--1063934 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1063880 TTGCAAACTA
1063890 TTAAAGCCTTCATTGTCCTATAT
1 TTAAAGCCTTCATTGTCCTATAT
*
1063913 TTAAAGCTTTCATTGTCCTATA
1 TTAAAGCCTTCATTGTCCTATA
1063935 CTTGCAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (23 bp):
TTAAAGCCTTCATTGTCCTATAT
Found at i:1064440 original size:73 final size:73
Alignment explanation
Indices: 1064348--1064550 Score: 185
Period size: 73 Copynumber: 2.8 Consensus size: 73
1064338 TTTCAGAAGC
** *
1064348 TTAATTTAGTTTGATTTATTGAAATTTGATACAAAGTAAAACAGCTTGTTCAATTATGCGTTTTA
1 TTAATTTAGTTCAATTTATTGAAATTTGATACAAAGTAAAACAGCTTATTCAATTATGCGTTTTA
1064413 AAAAAAAG
66 AAAAAAAG
* ** * * * *
1064421 TTAATTTAGTTCAATTTATTGAATTTTGATATTAAGTAGAACCGTTTATTCAATTATGTGTTTT-
1 TTAATTTAGTTCAATTTATTGAAATTTGATACAAAGTAAAACAGCTTATTCAATTATGCGTTTTA
** *
1064485 TTAAAAGG
66 AAAAAAAG
* * * * ** **
1064493 CTATTTTAGTTCAATTCATTG-AGTTTCGATATTAAGTAAAACAATTTATTCAAGTTAT
1 TTAATTTAGTTCAATTTATTGAAATTT-GATACAAAGTAAAACAGCTTATTCAA-TTAT
1064551 ATGTTTTGAG
Statistics
Matches: 108, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
71 4 0.04
72 46 0.43
73 58 0.54
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.44
Consensus pattern (73 bp):
TTAATTTAGTTCAATTTATTGAAATTTGATACAAAGTAAAACAGCTTATTCAATTATGCGTTTTA
AAAAAAAG
Found at i:1064524 original size:72 final size:72
Alignment explanation
Indices: 1064249--1064615 Score: 276
Period size: 72 Copynumber: 5.1 Consensus size: 72
1064239 AGTAAAATTA
* *
1064249 TTTATTTAATTATGTGTTTTTAAAAAGGTTAATTTAGTTCAATTTATT-AAGTTTTGATATTAAG
1 TTTATTCAATTATGTGTTTTTAAAAAGGCTAATTTAGTTCAATTTATTGAA-TTTTGATATTAAG
** *
1064313 CGAAACCG
65 TAAAACAG
* * *** * * ** * **
1064321 TTTATTTAGTTAT-ACATTTTCAGAA-GCTTAATTTAGTTTGATTTATTGAAATTTGATACAAAG
1 TTTATTCAATTATGTGTTTTTAAAAAGGC-TAATTTAGTTCAATTTATTGAATTTTGATATTAAG
1064384 TAAAACAG
65 TAAAACAG
* * * * * *
1064392 CTTGTTCAATTATGCGTTTTAAAAAAAAGTTAATTTAGTTCAATTTATTGAATTTTGATATTAAG
1 TTTATTCAATTATGTGTTTT-TAAAAAGGCTAATTTAGTTCAATTTATTGAATTTTGATATTAAG
* *
1064457 TAGAACCG
65 TAAAACAG
* * * * *
1064465 TTTATTCAATTATGTGTTTTTTAAAAGGCTATTTTAGTTCAATTCATTGAGTTTCGATATTAAGT
1 TTTATTCAATTATGTGTTTTTAAAAAGGCTAATTTAGTTCAATTTATTGAATTTTGATATTAAGT
*
1064530 AAAACAA
66 AAAACAG
* * * ** * * ** * *
1064537 TTTATTCAAGTTATATG-TTTTGAGAAGATTAAATTAATTTGATTTATTGAGTTGTGATATTAAG
1 TTTATTCAA-TTATGTGTTTTTAAAAAGGCTAATTTAGTTCAATTTATTGAATTTTGATATTAAG
1064601 TAAAATC-G
65 TAAAA-CAG
1064609 TTTATTC
1 TTTATTC
1064616 GGTGATATTA
Statistics
Matches: 227, Mismatches: 61, Indels: 14
0.75 0.20 0.05
Matches are distributed among these distances:
70 1 0.00
71 48 0.21
72 114 0.50
73 63 0.28
74 1 0.00
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.46
Consensus pattern (72 bp):
TTTATTCAATTATGTGTTTTTAAAAAGGCTAATTTAGTTCAATTTATTGAATTTTGATATTAAGT
AAAACAG
Found at i:1065408 original size:35 final size:35
Alignment explanation
Indices: 1065358--1065424 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
1065348 AGATTTAAAG
* *
1065358 ATGATAATCATAACTTACAAAAATATTTAAAGTTT
1 ATGATAATCAAAACTTACAAAAACATTTAAAGTTT
* *
1065393 ATGATTATCAAAACTTACATAAACATTTAAAG
1 ATGATAATCAAAACTTACAAAAACATTTAAAG
1065425 AATAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.34
Consensus pattern (35 bp):
ATGATAATCAAAACTTACAAAAACATTTAAAGTTT
Found at i:1065459 original size:9 final size:9
Alignment explanation
Indices: 1065445--1065579 Score: 70
Period size: 9 Copynumber: 15.6 Consensus size: 9
1065435 AACTTTGGAT
1065445 TATAACTTA
1 TATAACTTA
1065454 TATAACTTA
1 TATAACTTA
*
1065463 CATAA-TTCA
1 TATAACTT-A
1065472 TA-AA--TA
1 TATAACTTA
1065478 TATAACTTA
1 TATAACTTA
*
1065487 CATAA--TA
1 TATAACTTA
* *
1065494 CATAA-ATA
1 TATAACTTA
* *
1065502 TATATCATA
1 TATAACTTA
1065511 TCATAACTTA
1 T-ATAACTTA
*
1065521 CATAACTTA
1 TATAACTTA
*
1065530 TATAA-ATA
1 TATAACTTA
* *
1065538 TATATCATA
1 TATAACTTA
1065547 TCATAACTTA
1 T-ATAACTTA
*
1065557 CATAACTTA
1 TATAACTTA
*
1065566 CATAACTTA
1 TATAACTTA
*
1065575 CATAA
1 TATAA
1065580 ATAAATATCA
Statistics
Matches: 103, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
6 3 0.03
7 10 0.10
8 15 0.15
9 63 0.61
10 12 0.12
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (9 bp):
TATAACTTA
Found at i:1065483 original size:24 final size:24
Alignment explanation
Indices: 1065452--1065505 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
1065442 GATTATAACT
*
1065452 TATATAACTTACATAATTCATAAA
1 TATATAACTTACATAATACATAAA
1065476 TATATAACTTACATAATACATAAA
1 TATATAACTTACATAATACATAAA
1065500 TATATA
1 TATATA
1065506 TCATATCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (24 bp):
TATATAACTTACATAATACATAAA
Found at i:1065542 original size:36 final size:36
Alignment explanation
Indices: 1065446--1065570 Score: 172
Period size: 36 Copynumber: 3.6 Consensus size: 36
1065436 ACTTTGGATT
* *
1065446 ATAACTTATATAACTTACAT-AAT-TCATA-AATAT-
1 ATAACTTACATAACTTACATAAATAT-ATATCATATC
1065479 ATAACTTACATAA--TACATAAATATATATCATATC
1 ATAACTTACATAACTTACATAAATATATATCATATC
*
1065513 ATAACTTACATAACTTATATAAATATATATCATATC
1 ATAACTTACATAACTTACATAAATATATATCATATC
1065549 ATAACTTACATAACTTACATAA
1 ATAACTTACATAACTTACATAA
1065571 CTTACATAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 9
0.86 0.04 0.09
Matches are distributed among these distances:
31 5 0.06
32 6 0.07
33 17 0.21
34 13 0.16
36 41 0.50
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (36 bp):
ATAACTTACATAACTTACATAAATATATATCATATC
Found at i:1065564 original size:45 final size:45
Alignment explanation
Indices: 1065479--1065606 Score: 154
Period size: 45 Copynumber: 2.9 Consensus size: 45
1065469 TCATAAATAT
* * * *
1065479 ATAACTTACAT-AATACATA-AATAT-ATATCATATCATAACTTAC
1 ATAACTTACATAAATAAATATCATATAATAACTTA-CATAACTTAC
* * *
1065522 ATAACTTATATAAATATATATCATATCATAACTTACATAACTTAC
1 ATAACTTACATAAATAAATATCATATAATAACTTACATAACTTAC
*
1065567 ATAACTTACATAAATAAATATCATATAATAACTTCCATAA
1 ATAACTTACATAAATAAATATCATATAATAACTTACATAA
1065607 AACTTTGGAT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
43 10 0.14
44 7 0.10
45 50 0.68
46 6 0.08
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (45 bp):
ATAACTTACATAAATAAATATCATATAATAACTTACATAACTTAC
Found at i:1065598 original size:36 final size:36
Alignment explanation
Indices: 1065446--1065606 Score: 134
Period size: 45 Copynumber: 4.4 Consensus size: 36
1065436 ACTTTGGATT
* ** *
1065446 ATAACTTATATAACTTACAT-AATTCATA-AATAT-
1 ATAACTTACATAACTTACATAAATAAATATCATATA
* *
1065479 ATAACTTACATAA--TACATAAATATATATCATATC
1 ATAACTTACATAACTTACATAAATAAATATCATATA
*
1065513 ATAACTTACATAACTTATATAAATATATATCATATCATAACTTA
1 ATAACTTACATAACTTACAT-AA-ATA-A--ATATCAT-A--TA
1065557 CATAACTTACATAACTTACATAAATAAATATCATATA
1 -ATAACTTACATAACTTACATAAATAAATATCATATA
*
1065594 ATAACTTCCATAA
1 ATAACTTACATAA
1065607 AACTTTGGAT
Statistics
Matches: 105, Mismatches: 9, Indels: 25
0.76 0.06 0.18
Matches are distributed among these distances:
31 5 0.05
32 6 0.06
33 16 0.15
34 13 0.12
36 16 0.15
37 4 0.04
38 3 0.03
39 1 0.01
40 7 0.07
41 7 0.07
42 2 0.02
43 3 0.03
44 3 0.03
45 19 0.18
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (36 bp):
ATAACTTACATAACTTACATAAATAAATATCATATA
Found at i:1071324 original size:66 final size:65
Alignment explanation
Indices: 1071210--1071348 Score: 190
Period size: 66 Copynumber: 2.1 Consensus size: 65
1071200 TCACATTGCT
* * *
1071210 CAACTTAAAGTGGAGGTAGCATCGAGAGAAGCAAAGGCTCAAATAAAATATGAAGAACTCCAGCT
1 CAACTTAAAGTGGAGGCAGCAGCGAGAGAAGCAAAGGC-CAAAAAAAATATGAAGAACTCCAGCT
1071275 A
65 A
* * *
1071276 CAACTTAAAGTGGAGGCAGCAGCGAGGGAAGCAGAGG-CAAGCAAAAAATATGACGAACTCCAGC
1 CAACTTAAAGTGGAGGCAGCAGCGAGAGAAGCAAAGGCCAA--AAAAAATATGAAGAACTCCAGC
1071340 TA
64 TA
1071342 CAACTTA
1 CAACTTA
1071349 CGAATATGAT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
64 3 0.05
66 62 0.95
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.14
Consensus pattern (65 bp):
CAACTTAAAGTGGAGGCAGCAGCGAGAGAAGCAAAGGCCAAAAAAAATATGAAGAACTCCAGCTA
Found at i:1071744 original size:43 final size:42
Alignment explanation
Indices: 1071697--1071841 Score: 168
Period size: 43 Copynumber: 3.4 Consensus size: 42
1071687 AGAACATGAC
1071697 CTTTAGCGGCGTTTTTGGGTAAAGAGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCGTTTTTGGG-AAAGAGCCGCTAAAGGTCATGTT
* *
1071740 CTTTAGCGACATTTTTGGGGAAAGCA-CCGCTAAAGGTCATGTT
1 CTTTAGCGGCGTTTTT-GGGAAAG-AGCCGCTAAAGGTCATGTT
* * * *
1071783 CTGTAGCGGCGTTTGTAGGGAAA-ACGCCGCTAAATGTCTTGTT
1 CTTTAGCGGCGTTT-TTGGGAAAGA-GCCGCTAAAGGTCATGTT
*
1071826 CTATAGCGGCGTTTTT
1 CTTTAGCGGCGTTTTT
1071842 CCACATAAAT
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 80 0.92
44 5 0.06
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.32
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTGGGAAAGAGCCGCTAAAGGTCATGTT
Found at i:1074921 original size:23 final size:23
Alignment explanation
Indices: 1074895--1074944 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1074885 TATCCCCACA
*
1074895 TGGAGTGTAG-GGTTGGACGGAGT
1 TGGAGTGTAGAGGCTGGACGG-GT
*
1074918 TGGAGTGTAGAGGCTGGATGGGT
1 TGGAGTGTAGAGGCTGGACGGGT
1074941 TGGA
1 TGGA
1074945 TTTGATACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.18, C:0.04, G:0.52, T:0.26
Consensus pattern (23 bp):
TGGAGTGTAGAGGCTGGACGGGT
Found at i:1075500 original size:17 final size:18
Alignment explanation
Indices: 1075449--1075506 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
1075439 GCAATAAGTG
*
1075449 ACGTTTTGAAAATTAATA
1 ACGTTTTGAAAATGAATA
*
1075467 ACGTTTTGAAAAAGAATA
1 ACGTTTTGAAAATGAATA
* *
1075485 AC-TTTTGAATATGAATC
1 ACGTTTTGAAAATGAATA
1075502 ACGTT
1 ACGTT
1075507 GAAATTAATC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 14 0.41
18 20 0.59
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (18 bp):
ACGTTTTGAAAATGAATA
Found at i:1083393 original size:6 final size:6
Alignment explanation
Indices: 1083382--1083416 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
1083372 TGATATTAAC
1083382 AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT
1083417 CAGTCAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:1085827 original size:35 final size:35
Alignment explanation
Indices: 1085771--1085844 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
1085761 AAACTAGACG
* *
1085771 TTTTGTAATATTTTATTGTTCTAACACATTTAATA
1 TTTTCTAATATTTTATGGTTCTAACACATTTAATA
*
1085806 TTTTCTAATATTTTATGGTTCTGACACATTTAATA
1 TTTTCTAATATTTTATGGTTCTAACACATTTAATA
1085841 TTTT
1 TTTT
1085845 TTGATAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.09, G:0.07, T:0.55
Consensus pattern (35 bp):
TTTTCTAATATTTTATGGTTCTAACACATTTAATA
Found at i:1089140 original size:37 final size:37
Alignment explanation
Indices: 1089098--1089174 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
1089088 ATGCCATGTC
*
1089098 CCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTG
1 CCAGACATGGTCATACAGGGGACCTCTCATCTCGGTG
*
1089135 CCAGACATGGTCATACATGGGACCTCTCATCTCGGTG
1 CCAGACATGGTCATACAGGGGACCTCTCATCTCGGTG
1089172 CCA
1 CCA
1089175 ATGACATGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.21, C:0.31, G:0.25, T:0.23
Consensus pattern (37 bp):
CCAGACATGGTCATACAGGGGACCTCTCATCTCGGTG
Found at i:1089194 original size:87 final size:87
Alignment explanation
Indices: 1089048--1089214 Score: 228
Period size: 87 Copynumber: 1.9 Consensus size: 87
1089038 ATGCCATATC
* * ** *
1089048 CCAGATATGGTCTTACATGGGAGTTATCATATAGGTGTCCATGCCATGTCCCAGACATGGTCTTA
1 CCAGACATGGTCATACATGGGACCTATCATATAGGTGTCCATGACATGTCCCAGACATGGTCTTA
1089113 CAGGGGACCTCTCATCTCGGTG
66 CAGGGGACCTCTCATCTCGGTG
* * * *
1089135 CCAGACATGGTCATACATGGGACCTCTCATCTCGGTG-CCAATGACATGTCCGAGACATGGTCTT
1 CCAGACATGGTCATACATGGGACCTATCATATAGGTGTCC-ATGACATGTCCCAGACATGGTCTT
*
1089199 ACATGGGACCTCTCAT
65 ACAGGGGACCTCTCAT
1089215 AATCTNNNNN
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
86 2 0.03
87 67 0.97
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (87 bp):
CCAGACATGGTCATACATGGGACCTATCATATAGGTGTCCATGACATGTCCCAGACATGGTCTTA
CAGGGGACCTCTCATCTCGGTG
Found at i:1091944 original size:22 final size:22
Alignment explanation
Indices: 1091919--1091963 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1091909 TAGTTTTTCT
1091919 CTTAAATGAATCTGGACACTGG
1 CTTAAATGAATCTGGACACTGG
1091941 CTTAAATGAATCTGGACACTGG
1 CTTAAATGAATCTGGACACTGG
1091963 C
1 C
1091964 ACTTAATCCT
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:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (22 bp):
CTTAAATGAATCTGGACACTGG
Found at i:1093235 original size:27 final size:27
Alignment explanation
Indices: 1093197--1093442 Score: 336
Period size: 27 Copynumber: 9.1 Consensus size: 27
1093187 CGTGGGCAAG
1093197 TGATCGAAATACCCTCGAAGGGTAAAA
1 TGATCGAAATACCCTCGAAGGGTAAAA
*
1093224 TGATCGAAATACCCTCGAAGGTTAAAA
1 TGATCGAAATACCCTCGAAGGGTAAAA
*
1093251 TGA-CTGAAATACCCTCGAAAGGTAAAA
1 TGATC-GAAATACCCTCGAAGGGTAAAA
*
1093278 TGATCAAAATACCCTCGAAGGGTAAAA
1 TGATCGAAATACCCTCGAAGGGTAAAA
*
1093305 TGACCGAAATACCCTCGAAGGGTAAAA
1 TGATCGAAATACCCTCGAAGGGTAAAA
* **
1093332 TGACCGAAATACCCTTAAAGGGTAAAA
1 TGATCGAAATACCCTCGAAGGGTAAAA
* *
1093359 TGATCGAAATACCCTCAAAAGGTAAAA
1 TGATCGAAATACCCTCGAAGGGTAAAA
* *
1093386 TGATCGAAATACCCCCAAAGGGTAAAA
1 TGATCGAAATACCCTCGAAGGGTAAAA
*
1093413 TGA-CTGAAATACCC-CCATAGGGTAAAA
1 TGATC-GAAATACCCTCGA-AGGGTAAAA
1093440 TGA
1 TGA
1093443 CTGATATACC
Statistics
Matches: 200, Mismatches: 15, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
26 4 0.02
27 195 0.98
28 1 0.00
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.18
Consensus pattern (27 bp):
TGATCGAAATACCCTCGAAGGGTAAAA
Found at i:1093842 original size:28 final size:28
Alignment explanation
Indices: 1093802--1093895 Score: 100
Period size: 28 Copynumber: 3.4 Consensus size: 28
1093792 ACTACACTGT
1093802 ACTGTTACTGTATTGGGCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
* * *
1093830 ACTGCTACTGTATTAGGCTCAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
* * * * *
1093858 CCTGATACTGCT-TAGGGCTTAGGCCCAG
1 ACTGTTACTG-TATTGGGCTAAGGCCCAC
1093886 ACTGTTACTG
1 ACTGTTACTG
1093896 CATGTCGTAT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 53 0.98
29 1 0.02
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (28 bp):
ACTGTTACTGTATTGGGCTAAGGCCCAC
Found at i:1096675 original size:18 final size:17
Alignment explanation
Indices: 1096638--1096671 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1096628 ATTTCATTTT
1096638 CACAAACCATTTTCAAA
1 CACAAACCATTTTCAAA
*
1096655 CACAAATCATTTTCAAA
1 CACAAACCATTTTCAAA
1096672 ACACTATGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (17 bp):
CACAAACCATTTTCAAA
Found at i:1100343 original size:13 final size:11
Alignment explanation
Indices: 1100307--1100337 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1100297 CTGTCCGTAT
1100307 TAATTTTTATA
1 TAATTTTTATA
*
1100318 TTATTTTTATA
1 TAATTTTTATA
1100329 TAATTTTTA
1 TAATTTTTA
1100338 AATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:1100503 original size:29 final size:30
Alignment explanation
Indices: 1100459--1100516 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
1100449 CTTAACAAGA
*
1100459 AAATGCCTCTACAAT-ATAACAAAATTAAT
1 AAATGCCTCTAAAATAATAACAAAATTAAT
*
1100488 AAATGCCTTTAAAATAATAACAAAATTAA
1 AAATGCCTCTAAAATAATAACAAAATTAA
1100517 CAATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.28
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAT
Found at i:1100549 original size:25 final size:23
Alignment explanation
Indices: 1100498--1100551 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 23
1100488 AAATGCCTTT
* *
1100498 AAAATAATAACAAAATTAACAAT
1 AAAATAATAACAAAAATAACAAC
*
1100521 AAAATAATATCCAAACAATAACAAC
1 AAAATAATA-ACAAA-AATAACAAC
1100546 AAAATA
1 AAAATA
1100552 GTAGCAACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 9 0.35
24 4 0.15
25 13 0.50
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.19
Consensus pattern (23 bp):
AAAATAATAACAAAAATAACAAC
Found at i:1113067 original size:27 final size:27
Alignment explanation
Indices: 1113020--1113353 Score: 342
Period size: 27 Copynumber: 12.4 Consensus size: 27
1113010 AGGCCGTAAC
**
1113020 AGTCATTTTATCTCCTA--GGGGTATAAT
1 AGTCATTTTA-C-CCTATGGGGGTATTTT
1113047 AGTCATTTTACCCTATGGGGGTA-TTT
1 AGTCATTTTACCCTATGGGGGTATTTT
*
1113073 CGATCATTTTACCCTATGGGGGTATTTT
1 AG-TCATTTTACCCTATGGGGGTATTTT
* * *
1113101 GGTCATTCTACCCTATGCGGGTA-TTT
1 AGTCATTTTACCCTATGGGGGTATTTT
*
1113127 CGATCATTTTACCCTAT-GGGGTA-TTT
1 AG-TCATTTTACCCTATGGGGGTATTTT
* **
1113153 CGATCATTTTACCCTATGGAAGTATTTT
1 AG-TCATTTTACCCTATGGGGGTATTTT
** *
1113181 AGTCATTTTACCCTATAAGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTT
* *
1113208 AGTCATTTTACCTTATGGGGTTATTTTT
1 AGTCATTTTACCCTATGGGGGTA-TTTT
*
1113236 A-TCATTTTACCCTATGGGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTT
* * *
1113262 GGTCATTCTA-CCTATGAGGGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTT
* **
1113288 GGTCATTTTACTTTATGGGGGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTT
* *
1113315 AGTCATTTTATCCTATTGGGGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTT
1113342 AGTCATTTTACC
1 AGTCATTTTACC
1113354 TATTTTGGGG
Statistics
Matches: 258, Mismatches: 39, Indels: 20
0.81 0.12 0.06
Matches are distributed among these distances:
25 4 0.02
26 58 0.22
27 184 0.71
28 12 0.05
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.44
Consensus pattern (27 bp):
AGTCATTTTACCCTATGGGGGTATTTT
Found at i:1113178 original size:80 final size:81
Alignment explanation
Indices: 1113049--1113353 Score: 384
Period size: 80 Copynumber: 3.8 Consensus size: 81
1113039 GGTATAATAG
*
1113049 TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGGTCATTCTACCC
1 TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTAGTCATTCTACCC
*
1113114 TATGCGGGTATTTCGA
66 TATGAGGGTATTTCGA
** *
1113130 TCATTTTACCCTAT-GGGGTATTTCGATCATTTTACCCTATGGAAGTATTTTAGTCATTTTACCC
1 TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTAGTCATTCTACCC
*
1113194 TATAAGGGTATTTC-A
66 TATGAGGGTATTTCGA
* * ** **
1113209 GTCATTTTACCTTATGGGGTTATTTTTATCATTTTACCCTATGGGGGTATTTCGGTCATTCTA-C
1 -TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTAGTCATTCTACC
* *
1113273 CTATGAGGGTATTTTGG
65 CTATGAGGGTATTTCGA
** * * * *
1113290 TCATTTTACTTTATGGGGGTATTT-TAGTCATTTTATCCTATTGGGGTATTTTAGTCATTTTACC
1 TCATTTTACCCTATGGGGGTATTTCGA-TCATTTTACCCTATGGGGGTATTTTAGTCATTCTACC
1113354 TATTTTGGGG
Statistics
Matches: 194, Mismatches: 25, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
79 3 0.02
80 137 0.71
81 54 0.28
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.45
Consensus pattern (81 bp):
TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTAGTCATTCTACCC
TATGAGGGTATTTCGA
Found at i:1113369 original size:26 final size:26
Alignment explanation
Indices: 1113313--1113370 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
1113303 TGGGGGTATT
*
1113313 TTAGTCATTTTATCCTATTGGGGTATT
1 TTAGTCATTTTATCCTATTGGGG-ATC
1113340 TTAGTCATTTTA-CCTATTTTGGGG-TC
1 TTAGTCATTTTATCCTA--TTGGGGATC
1113366 TTAGT
1 TTAGT
1113371 GTAGATATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 10 0.36
27 12 0.43
28 6 0.21
ACGTcount: A:0.17, C:0.12, G:0.19, T:0.52
Consensus pattern (26 bp):
TTAGTCATTTTATCCTATTGGGGATC
Found at i:1116550 original size:598 final size:593
Alignment explanation
Indices: 1115382--1116560 Score: 1833
Period size: 598 Copynumber: 2.0 Consensus size: 593
1115372 AGTCGACAAA
* * * * *
1115382 CCCCAATTTTGGCTTTCTCTGTTCGCTGGTTTTTGGGTTTCTCGTTACGCACCTAGGCAAAATCG
1 CCCCAATTTCGGCTTTCTCTGTTCGCTGGTTTTTGGGTTCCTCATTACACACCTAGGCAAAATCA
* * ** *
1115447 ATGTAGAACTCAACAATCGAGTATTCTGGTACCTAGATTGACAATTTACATGATTTTTTAACCAA
66 ATGTAGAACTCAACAATCAAGTATTCTGGTACCTAGATTGACAATTCACACAAGTTTTTAACCAA
1115512 AATCTTACCAAACCCAAATGAAAAATTCACAAGAGCAACACTAATTGAACCTATATTCAACCATT
131 AATCTTACCAAACCCAAATGAAAAATTCACAAGAGCAACACTAATTGAACCTATATTCAACCATT
* * *
1115577 AACAACCCCTAAATGATATGAAACACTTACACTTGAATGAAAACACCATACAACTCTTAATTTGC
196 AACAACCCCTAAATGATATGAAACACTTACACTTGAATGAAAACACCACACAACTCCTAATTAGC
* *
1115642 TGGTAGATGGACTATCTCATGAAATTCAACTAAAACCAATCAATCGGTTAACATCGATACAACTC
261 TAGTAGATGGACTATCCCATGAAATTCAACTAAAACCAATCAATCGGTTAACATCGATACAACTC
* *
1115707 CACCACCACACCTCAACAAGTTGAAAACTAAAGAAGAAAAACTCCATAACATAAGAGAAGAAGTC
326 CACCACCACACCTCAACAAGTTGAAAACTAAAGAAGAAAAACACCAAAACATAAGAGAAGAAGTC
* *
1115772 AAGACTTACACACGAATCAGGTTGTAATCTATACAATCAAACATCACCACCGAACTTGAATAGTA
391 AAGACTTACACACGAATCAGGTTGCAATCTATACAATCAAACATCACCACCAAACTTGAATAGTA
* * * *
1115837 AGAACAATGGAAGTAAGGGCTCTAAAGACCAAGAAACCAACAGAGTAAGTTGCTACCAAGAACTC
456 AGAACAATGGAAGTAAGGGCACTAAAGACCAAGAAACCAAAAGAGCAAGTTGATACCAAGAACTC
* *
1115902 ACATGAAAAGAAAGAAAATAAAACTGGGAAAAATAAAAGGAACGTGGAAAAAGGGAAGAGATGGC
521 ACATGAAAAGAAAGAAAATAAAACTGGGAAAAACAAAAGGAACATGG-AAAAGGGAAGAGATGGC
1115967 GTTGACAGG
585 GTTGACAGG
* *
1115976 CCCCAATTTCGGCTTTCTCTGTTTGCT-GTTTTTATGGTTCCTCATTACACACCTAGGCAAAATC
1 CCCCAATTTCGGCTTTCTCTGTTCGCTGGTTTTT-GGGTTCCTCATTACACACCTAGGCAAAATC
1116040 AATGTAGAACTCAACAATCAAGTATTCTGGTACCTAGATTGACAATTCACACAAGTTTTTAACCA
65 AATGTAGAACTCAACAATCAAGTATTCTGGTACCTAGATTGACAATTCACACAAGTTTTTAACCA
* * * * *
1116105 AAGTCTTATCAAACCCAAATGACAAGTTCACAAGAGCAACACTAATTGGACCTATATTCAACCAT
130 AAATCTTACCAAACCCAAATGAAAAATTCACAAGAGCAACACTAATTGAACCTATATTCAACCAT
*
1116170 TAACAACCCCTAAAATGATATG-AACACTTACCCTTGAATGAAAACAACACCACACAACTCCTAA
195 TAACAACCCCT-AAATGATATGAAACACTTACACTTGAATG--AA-AACACCACACAACTCCTAA
* * * * * * *
1116234 TTAGCTAGTAGATGGATTGTCCCGTGAACTTCACCTAAAACCGATCAATCGGTTAATATCGATAC
256 TTAGCTAGTAGATGGACTATCCCATGAAATTCAACTAAAACCAATCAATCGGTTAACATCGATAC
* *
1116299 AACTCCCCCACCACACCTCAACAAAGTTGAAAACTGAAGAAGAAAAACACCAAAACATAAGA-AA
321 AACTCCACCACCACACCTCAAC-AAGTTGAAAACTAAAGAAGAAAAACACCAAAACATAAGAGAA
* * *
1116363 GGATGTCAAGACTTACACACGAATCAGGTTGCAATCTATACAATCGAACATCACTACCAAACTTG
385 -GAAGTCAAGACTTACACACGAATCAGGTTGCAATCTATACAATCAAACATCACCACCAAACTTG
* * *
1116428 AATAGTAAGAACATTGGAAGTAAGGGCACTAAAGACCAAGAAACCAAAAGAGCAATTTGATACTA
449 AATAGTAAGAACAATGGAAGTAAGGGCACTAAAGACCAAGAAACCAAAAGAGCAAGTTGATACCA
1116493 AGAACTCACATGAAAAGAAAGAAAATAAAACTGGGAAAAACAAAAGGAACATGGAAAAGGGAAGA
514 AGAACTCACATGAAAAGAAAGAAAATAAAACTGGGAAAAACAAAAGGAACATGGAAAAGGGAAGA
1116558 GAT
579 GAT
1116561 TTTTGGTATA
Statistics
Matches: 530, Mismatches: 48, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
593 6 0.01
594 198 0.37
595 10 0.02
596 2 0.00
597 109 0.21
598 205 0.39
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.22
Consensus pattern (593 bp):
CCCCAATTTCGGCTTTCTCTGTTCGCTGGTTTTTGGGTTCCTCATTACACACCTAGGCAAAATCA
ATGTAGAACTCAACAATCAAGTATTCTGGTACCTAGATTGACAATTCACACAAGTTTTTAACCAA
AATCTTACCAAACCCAAATGAAAAATTCACAAGAGCAACACTAATTGAACCTATATTCAACCATT
AACAACCCCTAAATGATATGAAACACTTACACTTGAATGAAAACACCACACAACTCCTAATTAGC
TAGTAGATGGACTATCCCATGAAATTCAACTAAAACCAATCAATCGGTTAACATCGATACAACTC
CACCACCACACCTCAACAAGTTGAAAACTAAAGAAGAAAAACACCAAAACATAAGAGAAGAAGTC
AAGACTTACACACGAATCAGGTTGCAATCTATACAATCAAACATCACCACCAAACTTGAATAGTA
AGAACAATGGAAGTAAGGGCACTAAAGACCAAGAAACCAAAAGAGCAAGTTGATACCAAGAACTC
ACATGAAAAGAAAGAAAATAAAACTGGGAAAAACAAAAGGAACATGGAAAAGGGAAGAGATGGCG
TTGACAGG
Found at i:1123334 original size:20 final size:20
Alignment explanation
Indices: 1123303--1123369 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
1123293 TGTAGCATGC
*
1123303 ACACGGGCATGTAAACCATT
1 ACACGAGCATGTAAACCATT
*
1123323 ACATGAGCATGTAAACCATT
1 ACACGAGCATGTAAACCATT
* * *
1123343 ACACGGGCATGTAGACCATC
1 ACACGAGCATGTAAACCATT
1123363 ACACGAG
1 ACACGAG
1123370 AGTGTAGACA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (20 bp):
ACACGAGCATGTAAACCATT
Found at i:1125464 original size:656 final size:656
Alignment explanation
Indices: 1123985--1126330 Score: 3326
Period size: 656 Copynumber: 3.6 Consensus size: 656
1123975 TGTCGTGTGC
**
1123985 AGGGTGGACGAAGAGGTGTTTGGATGGTTGGGGTGTCTTTTTGACTTAATGCATTCGGTTTGCAT
1 AGGGTGGACGAAGAGGTGTTTGGATGGTTGGGGTGGGTTTTTGACTTAATGCATTCGGTTTGCAT
* *
1124050 TTGAGCATATGTGTCTGATTATGAAATTTTCAAATTGTTTGCGAATGGTATATTAATTTGAAGTG
66 TTGAGCATATGTGTCTGATTATGAAAATTTCAAATTGTTTGCGAATGGTATATTAATTTGATGTG
* *
1124115 -TCTGTACCTCTGTTTACCGCTTCAAGGTTTTTATGCTCTGTCTATGCGTTCTTATCTAGGATAA
131 TTC-GTACCTCTGTTTACCACTTCAAGGTTTTTATGCTCTGTCTATGTGTTCTTATCTAGGATAA
** * * * *
1124179 TTGTTTTTGAAATCTCGTCTTTTGTCATTCATTTTTGGTTTCAAACACACACTGAGCTCCCGTAG
195 TTGTTTTTGAAATCTCACCTTTTGTCATTCATTTTTGGTTTCAGACTCACACTGAACTCGCGTAG
* * * * * * * *
1124244 CTCGCCTTCCTTTAGTTTCTCTATTTCAGGTAACTCGTGGTTTAAGGCTAGACTCAATAGTCGGA
260 CTCACCTCCCTTCAGTTTCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCGGA
* * *
1124309 GGTCTCAGAGAGATAGTGTTTGATTCAATTTAAGTAAAATTTTTATATA-TTTTATACAGTTGGT
325 GGTCTCAGAGAGATAGTGTTTGATTCGATTTAAGTAAAATTTTCATA-AGTTTTATACGGTTGGT
* * *
1124373 TTAAGACTGCTTGTAAAGCGATTATATAAACTGTGGTACAAAGTTTTTATGTTGGACTTTTGTAA
389 TTAAGACTGTTTCTAAAGCGATTATATAAACTGTGGTACAAAGTTTTTATGTTGGACTTTCGTAA
* * * * *
1124438 AGTGTTATTTGGACTAAACTTTAGAAATTGTGGATTTTATGGCTGAATGTTTTGACGCCAGTTTA
454 AGTGTTATTTGGATTGAACTTTAGAAACTGTGGATTTTATGTCTGAATGTTTTGACGCCGGTTTA
* *
1124503 ATATTTGTTTCAAAACATAGCTAAGTTTTATTTAGTTTCCTTAAGTTGAAATGAAGAAAAGGGTT
519 ATA-TTGTTTCAAAACATAGCTAAGTTTTATTTAGTTTCCTTAAGTTGAAATGAACAAAAGGATT
* *
1124568 TTCCTGATTTGAATTAAAGTTTTTGTTTCCGCCACCATTGGTGGCTAAATGTAACCT-TCAGAAT
583 TTCTTGATTTGAATTAAAGTTTTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCTCT-AGAAT
*
1124632 CCGGTCTAAA
647 TCGGTCTAAA
* * * * *
1124642 AGGGTGGACGAAGAGGTGTTTGAATGGTTGGGGTGGGTTTTTTACTTAACGTATTCGGTTTGTAT
1 AGGGTGGACGAAGAGGTGTTTGGATGGTTGGGGTGGGTTTTTGACTTAATGCATTCGGTTTGCAT
* * * * *
1124707 TTTAGCATATGTGTCTGATGATGAAATTTTCAAATTGTTTGCGAATAGTATATTAATTTAATGTG
66 TTGAGCATATGTGTCTGATTATGAAAATTTCAAATTGTTTGCGAATGGTATATTAATTTGATGTG
* * * *
1124772 TTCGTACCTATGTTTATCACTTTAAGG-TTCTATGCTCTGTCTATGTGTTCTTATCTAGGATAAT
131 TTCGTACCTCTGTTTACCACTTCAAGGTTTTTATGCTCTGTCTATGTGTTCTTATCTAGGATAAT
* *
1124836 TGTTTCTGAAATCACACCTTTTGTCATTCATTTTTGGTTTCAGACTCACACTGAACTCGCGTAGC
196 TGTTTTTGAAATCTCACCTTTTGTCATTCATTTTTGGTTTCAGACTCACACTGAACTCGCGTAGC
* * * * * * * *
1124901 CCACCTTCCTTTAGTTTCTCTCTTTCAAGTAACTCGTCGTTTGAGGTTGGACTCGCCAGTCGGAT
261 TCACCTCCCTTCAGTTTCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCGGAG
*
1124966 GTCTTAGAGAGATAGTGTTTGACTT-GATTTAAGTAAAATTTTCATAAGTTTTATACGGTTGGTT
326 GTCTCAGAGAGATAGTGTTTGA-TTCGATTTAAGTAAAATTTTCATAAGTTTTATACGGTTGGTT
* * * *
1125030 TAAGACTGTTTCTAAAGCGACTATATAAACTGTTGTACAATGTTTTTATGTTGGACTTTCATAAA
390 TAAGACTGTTTCTAAAGCGATTATATAAACTGTGGTACAAAGTTTTTATGTTGGACTTTCGTAAA
* * *
1125095 GTGTTATTTGGATTGAACTTTAAAAACTGTAGATTTTATGTCTGAATGTTTTGATGCCGGTTTAA
455 GTGTTATTTGGATTGAACTTTAGAAACTGTGGATTTTATGTCTGAATGTTTTGACGCCGGTTTAA
* * * *
1125160 TATTGTTTCAAAACATAACTAAGTTTTATTTAGTTTCCTTCAGTTAAAACGAACAAAAGGATTTT
520 TATTGTTTCAAAACATAGCTAAGTTTTATTTAGTTTCCTTAAGTTGAAATGAACAAAAGGATTTT
*
1125225 CTTGATTTGAATTAAAGTTTTTGTTTCCACCACCTTTGGTGGCTAAATGTAACCTCTAGAATTCG
585 CTTGATTTGAATTAAAGTTTTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCTCTAGAATTCG
1125290 GTCTAAA
650 GTCTAAA
* ** * *
1125297 AGGGTGGACGAAGAGGTGTTTGGATGGTTAGGGTGGGTTTTTTTCTTAATGTATTCAGTTTGCAT
1 AGGGTGGACGAAGAGGTGTTTGGATGGTTGGGGTGGGTTTTTGACTTAATGCATTCGGTTTGCAT
* * *
1125362 TTGAGCATATGTGTCTGATTATGAAAATTACAAATTATTTGCAAATGGTATATTAATTTGATGTG
66 TTGAGCATATGTGTCTGATTATGAAAATTTCAAATTGTTTGCGAATGGTATATTAATTTGATGTG
* * * * * *
1125427 TTCATACCTCTGTTTACCGCTTCAAGGTTTTTATGCTCTATTTGTGTGTTCTTATCTGGGATAAT
131 TTCGTACCTCTGTTTACCACTTCAAGGTTTTTATGCTCTGTCTATGTGTTCTTATCTAGGATAAT
* * * *
1125492 TGTTTTTGAAATCTCACCTTTTGTAATTCATTTTTGCTTTCAGACTCACA-TTAAGCTTGCGTAG
196 TGTTTTTGAAATCTCACCTTTTGTCATTCATTTTTGGTTTCAGACTCACACTGAA-CTCGCGTAG
* * *
1125556 CTCAGCTCCCTTCAGTTTCTCTCTTTTAGGTAACTCGTGGTTTGAGGCTGGACTC-AGCAATCGG
260 CTCACCTCCCTTCAGTTTCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGA-CAGTCGG
* * *
1125620 AGGTCTCAGAGAGATAGTGTTTGATTCGGTTTAAGT-AAATATTTCATATGTTTTATACGGTTTG
324 AGGTCTCAGAGAGATAGTGTTTGATTCGATTTAAGTAAAAT-TTTCATAAGTTTTATACGGTTGG
* *
1125684 TTTAAGACTATTTTTAAAGCGATTATATAAACTGTGGTACAAAGTTTTTATGTTGGACTTTCGTA
388 TTTAAGACTGTTTCTAAAGCGATTATATAAACTGTGGTACAAAGTTTTTATGTTGGACTTTCGTA
* * *
1125749 AAATGTTATTTGGATTGAACTTTAGAAACTGTGGATTTTATGTCTCAATGTTTTGACGCTGGTTT
453 AAGTGTTATTTGGATTGAACTTTAGAAACTGTGGATTTTATGTCTGAATGTTTTGACGCCGGTTT
* * * **
1125814 AATATTATTTCAAAACATAGCTAAGTTTTATTTAGTTTTCTTAAGTTGAAATGCACAAAACTATT
518 AATATTGTTTCAAAACATAGCTAAGTTTTATTTAGTTTCCTTAAGTTGAAATGAACAAAAGGATT
* **
1125879 TTCTTGATTTGAATTAAAGTTTTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCACCGGAATT
583 TTCTTGATTTGAATTAAAGTTTTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCTCTAGAATT
1125944 CGGTCTAAA
648 CGGTCTAAA
** * * * *
1125953 ATTGTGGACCAAGAGGTGTTCGGATGGTTGGGGTGGGTTTTTGACTTAATACATTCGGTTTGCAC
1 AGGGTGGACGAAGAGGTGTTTGGATGGTTGGGGTGGGTTTTTGACTTAATGCATTCGGTTTGCAT
* * *
1126018 TTGAGCATATGTGTCTGATTATGAAAATTTCAGATTGTTTACGAATTGTATATTAATTTGATGTG
66 TTGAGCATATGTGTCTGATTATGAAAATTTCAAATTGTTTGCGAATGGTATATTAATTTGATGTG
* * * * *
1126083 TTCGTACATCTGTTTACCACTTCAAGGTTTTTATGCTTTGTCTATGTGTTCTAACCTGGGATAAT
131 TTCGTACCTCTGTTTACCACTTCAAGGTTTTTATGCTCTGTCTATGTGTTCTTATCTAGGATAAT
* * ** * * * *
1126148 TATTTTTTACCTCTCGCCTTTTGTCATTCATTTTT-TTTTCAGACTCATACTGAGCTCGCGTAGC
196 TGTTTTTGAAATCTCACCTTTTGTCATTCATTTTTGGTTTCAGACTCACACTGAACTCGCGTAGC
* *
1126212 TCACCTCCCTTCAATTTTTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCGGAG
261 TCACCTCCCTTCAGTTTCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCGGAG
*
1126277 GTCAT-AGAGAGATAGTGTTTGATTCGGTTTAAGTAAAATTTTCATAAGTTTTAT
326 GTC-TCAGAGAGATAGTGTTTGATTCGATTTAAGTAAAATTTTCATAAGTTTTAT
1126331 TTAGTTTCCT
Statistics
Matches: 1496, Mismatches: 180, Indels: 28
0.88 0.11 0.02
Matches are distributed among these distances:
655 396 0.26
656 958 0.64
657 140 0.09
658 2 0.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (656 bp):
AGGGTGGACGAAGAGGTGTTTGGATGGTTGGGGTGGGTTTTTGACTTAATGCATTCGGTTTGCAT
TTGAGCATATGTGTCTGATTATGAAAATTTCAAATTGTTTGCGAATGGTATATTAATTTGATGTG
TTCGTACCTCTGTTTACCACTTCAAGGTTTTTATGCTCTGTCTATGTGTTCTTATCTAGGATAAT
TGTTTTTGAAATCTCACCTTTTGTCATTCATTTTTGGTTTCAGACTCACACTGAACTCGCGTAGC
TCACCTCCCTTCAGTTTCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCGGAG
GTCTCAGAGAGATAGTGTTTGATTCGATTTAAGTAAAATTTTCATAAGTTTTATACGGTTGGTTT
AAGACTGTTTCTAAAGCGATTATATAAACTGTGGTACAAAGTTTTTATGTTGGACTTTCGTAAAG
TGTTATTTGGATTGAACTTTAGAAACTGTGGATTTTATGTCTGAATGTTTTGACGCCGGTTTAAT
ATTGTTTCAAAACATAGCTAAGTTTTATTTAGTTTCCTTAAGTTGAAATGAACAAAAGGATTTTC
TTGATTTGAATTAAAGTTTTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCTCTAGAATTCGG
TCTAAA
Found at i:1126760 original size:485 final size:486
Alignment explanation
Indices: 1125835--1126803 Score: 1246
Period size: 485 Copynumber: 2.0 Consensus size: 486
1125825 AAAACATAGC
* * * * * * *
1125835 TAAGTTTTATTTAGTTTTCTTAAGTTGAAATGCACAAAACTATTTTCTTGATTTGAATTAAAGTT
1 TAAGTTTTATTTAGTTTCCTTAAGTTGAAACGAACAAAACGACTTTCTAGAGTTGAATTAAAGTT
* **
1125900 TTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCACCGGAATTCGGTCTAAAATTGTGGACCAA
66 TTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCACCAGAATTCGGTCTAAAAGGGTGGACCAA
* *
1125965 GAGGTGTTCGGATGGTTGGGGTGGGTTTTTGACTTAATACATTCGGTTTGCACTTGAGCATATGT
131 AAGGTGTTCGAATGGTTGGGGTGGGTTTTTGACTTAATACATTCGGTTTGCACTTGAGCATATGT
* * * * *
1126030 GTCTGATTATGAAAATTTCAGATTGTTTACGAATTGTATATTAATTTGATGTGTTCGTACATCTG
196 GTCTGATTATGAAAATTTCAAATTGTTTACGAATGGTATATCAATTTGATGTATTCATACATCTG
* * * * * * **
1126095 TTTACCACTTCAAGGTTTTTATGCTTTGTCTATGTGTTCTAACCTGGGATAATTATTTTTTACCT
261 TTTACCACTTCAAGGTTTTTATACTCTATATATGTGTTCTAACCTGGGATAATTAGTTTTGAAAT
** * * * *
1126160 CTCGCCTTTTGTCATTCATTTTTTTTTCAGACTCATACTGAGCTCGCGTAGCTCACCTCCCTTCA
326 AACGCATTTTGTCATTCATTTTTGTTTCAGACTCAAACTGAACTCGCGTAGCTCACCTCCCTTCA
* * * *
1126225 ATTTTTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCGGAGGTCATAGAGAGAT
391 ATTTCTCTCTTACAGGTAACTCGTAGTTTGAGGCTGGACTCGACAGTCGGAGGGCATAGAGAGAT
*
1126290 AGTGTTTGATTCGGTTTAAGTAAAATTTTCA
456 AGTGTTTGATTCGATTTAAGTAAAATTTTCA
* * *
1126321 TAAGTTTTATTTAGTTTCCTTAAGTTGAAACGAACAAAAGGGCTTTCTAGAGTTGAATTAGAGTT
1 TAAGTTTTATTTAGTTTCCTTAAGTTGAAACGAACAAAACGACTTTCTAGAGTTGAATTAAAGTT
* * * * *
1126386 TTTGTTTTCTCTACCTTTGGTGGCTAAATGTAACCTCTAGAATTC-GTCTAAAAGGGTGGA-CAA
66 TTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCACCAGAATTCGGTCTAAAAGGGTGGACCAA
* * ** *
1126449 AATGGTGTTTGAATGGTTGGGGTGGGTTTTTTACTTAATGTATTCGGTTTGCATTTGAGCATATG
131 AA-GGTGTTCGAATGGTTGGGGTGGGTTTTTGACTTAATACATTCGGTTTGCACTTGAGCATATG
* * ** * *
1126514 TGTCTGATTATGGAATTTTCAAATTGTTTGTGAATGGTATATCAATTTGATGTATTCATACCTTT
195 TGTCTGATTATGAAAATTTCAAATTGTTTACGAATGGTATATCAATTTGATGTATTCATACATCT
* * * * *
1126579 GTTTACCATTTCAAGG-TTTTATACTCTATATGTGTGTTCTTATCTGGGATAATTGGTTTTGAAA
260 GTTTACCACTTCAAGGTTTTTATACTCTATATATGTGTTCTAACCTGGGATAATTAGTTTTGAAA
* * **
1126643 TAACGCATTTTGTCATTTATTTGTTGTTTCAGACTCAAATTGAACTCTTGTAGCTCACCTCCC-T
325 TAACGCATTTTGTCATTCATTT-TTGTTTCAGACTCAAACTGAACTCGCGTAGCTCACCTCCCTT
* * ** *
1126707 CTAGA-TTCTCTCTTACAGGTAACTCGTAGTTTGAGGTTGGACTTGGTAGTCGGAGGGCTTAGAG
389 C-A-ATTTCTCTCTTACAGGTAACTCGTAGTTTGAGGCTGGACTCGACAGTCGGAGGGCATAGAG
1126771 AGATAGTGTTTGATTCGATTTAAGTAAAATTTT
452 AGATAGTGTTTGATTCGATTTAAGTAAAATTTT
1126804 AACTTTTATT
Statistics
Matches: 410, Mismatches: 69, Indels: 9
0.84 0.14 0.02
Matches are distributed among these distances:
484 60 0.15
485 255 0.62
486 95 0.23
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (486 bp):
TAAGTTTTATTTAGTTTCCTTAAGTTGAAACGAACAAAACGACTTTCTAGAGTTGAATTAAAGTT
TTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCACCAGAATTCGGTCTAAAAGGGTGGACCAA
AAGGTGTTCGAATGGTTGGGGTGGGTTTTTGACTTAATACATTCGGTTTGCACTTGAGCATATGT
GTCTGATTATGAAAATTTCAAATTGTTTACGAATGGTATATCAATTTGATGTATTCATACATCTG
TTTACCACTTCAAGGTTTTTATACTCTATATATGTGTTCTAACCTGGGATAATTAGTTTTGAAAT
AACGCATTTTGTCATTCATTTTTGTTTCAGACTCAAACTGAACTCGCGTAGCTCACCTCCCTTCA
ATTTCTCTCTTACAGGTAACTCGTAGTTTGAGGCTGGACTCGACAGTCGGAGGGCATAGAGAGAT
AGTGTTTGATTCGATTTAAGTAAAATTTTCA
Found at i:1127685 original size:656 final size:651
Alignment explanation
Indices: 1126321--1128116 Score: 2364
Period size: 656 Copynumber: 2.7 Consensus size: 651
1126311 AAAATTTTCA
* * * *
1126321 TAAGTTTTATTTAGTTTCCTTAAGTTGAAACGAACAAAAGGGCTTTCTAGAGTTGAATT-AGAGT
1 TAAGTTTTATTTAGTTTTCTTAAGTTGAAACGAACAAAAGGGTTTTCTTGATTTGAATTAAG-GT
* * * * *
1126385 TTTTGTTTTCTCTACCTTTGGTGGCTAAATGTAACCTCTAGAATTCGTCTAAAAGGGTGGACAAA
65 TTTTGTTTCCACCACCTTTGGTGGCTAAATGTAACCTCTGGAATTCGTCTAAAAGGGTGGACAAG
* * *
1126450 ATGGTGTTTGAATGGTTGGGGTGGGTTTTTT-ACTTAATGTATTCGGTTTGCATTTGAGCATATG
130 A-GGTGTTTGGATGGTTGGGGT-GGTTTTTTGACTTAATGCATTCGGTTTGCATTTGAGCAAATG
* * * * *
1126514 TGTCTGATTATGGAATTTTCAAATTGTTTGTGAATGGTATATCAATTTGATGTATTCATACCTTT
193 TGTCTGATTATGAAATTTTCAAATTGTTTGTGAATGGTATATTAATTTGATGTGTTCGTACCTCT
** * *
1126579 GTTTACCATTTCAAGG-TTTTATACTCTATATGTGTGTTCTTATCTGGGATAATTGGTTTTGAAA
258 GTTTACCGCTTCAAGGTTTTTATGCTCTATATGTGTGTTCTTATCTGGGATAATTGTTTTTGAAA
** * * * * * * *
1126643 TAACGCATTTTGTCATTTATTTGTTGTTTCAGACTCAAATTGAACTCT-TGTAGCTCACCTCCCT
323 TCTCGCCTTTTGTCATTCATTT-TTGTTTCAAACTCAAACTGAGCT-TGCGTAGCTCACCTCCTT
* * * * * ** * * *
1126707 CTAGATTCTCTCTTACAGGTAACTCGTAGTTTGAGGTTGGACTTGGTAGTCGGAGGGCTTAGAGA
386 C-AGTTTCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCAGAGGTCTCAGAGA
*
1126772 GATAGTGTTTGATTCGATTTAAGTAAAATTTT-A-ACTTTTATTCTGTTGGTTGAAGACTGTTTC
450 GATAGTGTTTGATTCGATTTAAGTAAAATTTTCATACTTTTATACTGTTGGTTGAAGACTGTTTC
* * * * * *
1126835 TAAAGCGATTATATAATCTGTGGTACACAGTTTTTATGTTGGACTTTCGTAAAGTGTTATTTGGA
515 TAAAGCGATTATATAAGCTGTGCTACAAAGTTTTTATGTTGAACTTTCATAAAGTATTATTTGGA
* * * *
1126900 CTGAACTTTAGAAACTGTACATTTTATGTTTGAATGTTTTGATGCCGGTTTAATATTGTTTCAAA
580 CTGAACTTTAGAAACTATACATTTTATGTATGAATGTTTTGATGCCAGTTTAATATTATTTCAAA
1126965 ACATAGC
645 ACATAGC
*
1126972 TAAGTTTTATTTAGTTTTCTTAAGTTGATACGAACAAAAGGGTTTTCTTGATTTGAATTAAGGTT
1 TAAGTTTTATTTAGTTTTCTTAAGTTGAAACGAACAAAAGGGTTTTCTTGATTTGAATTAAGGTT
** *
1127037 TTTGTTTCCACCACCTTTGGTGGCTAAATGTAACCTCTGGAATTCAACCTAAAAGGGTGGACGAG
66 TTTGTTTCCACCACCTTTGGTGGCTAAATGTAACCTCTGGAATTC-GTCTAAAAGGGTGGAC-AA
*
1127102 GAGGTGTTTGGATGGTTGGGGTGGTTTTTTGACTTAATGCATTCGGTTTGCATTTGAGCAGATGT
129 GAGGTGTTTGGATGGTTGGGGTGGTTTTTTGACTTAATGCATTCGGTTTGCATTTGAGCAAATGT
* *
1127167 GTCTGATTATGAAATTTTCAAATTATTTGTGAACGGTATATTAATTTGATGTGTTCGTACCTCTG
194 GTCTGATTATGAAATTTTCAAATTGTTTGTGAATGGTATATTAATTTGATGTGTTCGTACCTCTG
* *
1127232 TTTACCGCGTCAAGGTTTTTATGCTCTATCTGTGTGTTCTTATCTGGGATAATTGTTTTTGAAAT
259 TTTACCGCTTCAAGGTTTTTATGCTCTATATGTGTGTTCTTATCTGGGATAATTGTTTTTGAAAT
* *
1127297 CTCTCCTTTTGTCATTCATTTTTGGTTTCAAACTCACACTGAGCTTGCGTAGCTCACCTCCTTTC
324 CTCGCCTTTTGTCATTCATTTTT-GTTTCAAACTCAAACTGAGCTTGCGTAGCTCACCTCC-TTC
* * * ** *
1127362 AGTTTCTCTCTTTTAGGTAACTCATGGTTTGAGCCTACACTCGACAGTCAAAGGTCTCAGAGAGA
387 AGTTTCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCAGAGGTCTCAGAGAGA
* * * * * * *
1127427 TAGTGTTTGATTCGGTATAAGTAAATTTTTCATATGTTTTATAC-GATTTGTTTAAGACTGTTTG
452 TAGTGTTTGATTCGATTTAAGTAAAATTTTCATA-CTTTTATACTG-TTGGTTGAAGACTGTTTC
* * *
1127491 TAAAGCGATTGTATAAGCTGTGCTACAAATTTTTTATGTTGAACTTTCATAAAGTATTATTTTGA
515 TAAAGCGATTATATAAGCTGTGCTACAAAGTTTTTATGTTGAACTTTCATAAAGTATTATTTGGA
* * **
1127556 TTGAACTTTCGAAACTATGGATTTTATGTATGAATGTTTTGATGCCAGTTTAATATTATTTCAAA
580 CTGAACTTTAGAAACTATACATTTTATGTATGAATGTTTTGATGCCAGTTTAATATTATTTCAAA
1127621 ACATAGC
645 ACATAGC
* * * * *
1127628 TAAGTTTTATTTAGTTTTCTTAAGTTGAAATGCACAAAAGTGTTTTCTTGATTTGAATTAAAGAT
1 TAAGTTTTATTTAGTTTTCTTAAGTTGAAACGAACAAAAGGGTTTTCTTGATTTGAATTAAGGTT
* * * *
1127693 TTTGTTTCCGCCACCTTTGGTGGCTAAATGTAACCTCCGAAATTCGGTCTAAAATGGTGGACCAA
66 TTTGTTTCCACCACCTTTGGTGGCTAAATGTAACCTCTGGAATTC-GTCTAAAAGGGTGGA-CAA
* * *
1127758 GAGGTGTTTGGATGGTTGGGGTGGGTTTTTGACTTAATACATTCGGTTTGCATTTAAGCAAATGT
129 GAGGTGTTTGGATGGTTGGGGTGGTTTTTTGACTTAATGCATTCGGTTTGCATTTGAGCAAATGT
* * *
1127823 GTCTTATTATGAAATTTTCAAATTGTTTGCGAATGGTATATTAATTTGATGTGTTCGTACCTCTA
194 GTCTGATTATGAAATTTTCAAATTGTTTGTGAATGGTATATTAATTTGATGTGTTCGTACCTCTG
* * * * * * * * *
1127888 TTTACCGCTTTAATGTTTTTATGCTCTGTTTGTCTGTTCTGACCTGGGATAATTATTTTTGACAT
259 TTTACCGCTTCAAGGTTTTTATGCTCTATATGTGTGTTCTTATCTGGGATAATTGTTTTTGAAAT
* * * *
1127953 CTCGCCTTTTGTCATTCATTTTTTGTTTCAAACTCATACTAAGCTCGCATAGCTCACCTCCCTTC
324 CTCGCCTTTTGTCATTCA-TTTTTGTTTCAAACTCAAACTGAGCTTGCGTAGCTCACCT-CCTTC
* * *
1128018 AATTTCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCAGATGTCACAGAGAGA
387 AGTTTCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCAGAGGTCTCAGAGAGA
* *
1128083 TAATGTTTGATTTGATTTAAGTAAAATTTTCATA
452 TAGTGTTTGATTCGATTTAAGTAAAATTTTCATA
1128117 AGTTGTATTT
Statistics
Matches: 997, Mismatches: 133, Indels: 25
0.86 0.12 0.02
Matches are distributed among these distances:
651 106 0.11
652 140 0.14
653 170 0.17
654 3 0.00
655 2 0.00
656 568 0.57
657 8 0.01
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.42
Consensus pattern (651 bp):
TAAGTTTTATTTAGTTTTCTTAAGTTGAAACGAACAAAAGGGTTTTCTTGATTTGAATTAAGGTT
TTTGTTTCCACCACCTTTGGTGGCTAAATGTAACCTCTGGAATTCGTCTAAAAGGGTGGACAAGA
GGTGTTTGGATGGTTGGGGTGGTTTTTTGACTTAATGCATTCGGTTTGCATTTGAGCAAATGTGT
CTGATTATGAAATTTTCAAATTGTTTGTGAATGGTATATTAATTTGATGTGTTCGTACCTCTGTT
TACCGCTTCAAGGTTTTTATGCTCTATATGTGTGTTCTTATCTGGGATAATTGTTTTTGAAATCT
CGCCTTTTGTCATTCATTTTTGTTTCAAACTCAAACTGAGCTTGCGTAGCTCACCTCCTTCAGTT
TCTCTCTTTCAGGTAACTCGTGGTTTGAGGCTGGACTCGACAGTCAGAGGTCTCAGAGAGATAGT
GTTTGATTCGATTTAAGTAAAATTTTCATACTTTTATACTGTTGGTTGAAGACTGTTTCTAAAGC
GATTATATAAGCTGTGCTACAAAGTTTTTATGTTGAACTTTCATAAAGTATTATTTGGACTGAAC
TTTAGAAACTATACATTTTATGTATGAATGTTTTGATGCCAGTTTAATATTATTTCAAAACATAG
C
Found at i:1129040 original size:24 final size:25
Alignment explanation
Indices: 1129012--1129058 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
1129002 TCTGACCCAA
*
1129012 TTTTACTGGAATATG-AATGGAAGC
1 TTTTACTGGAATAAGTAATGGAAGC
* *
1129036 TTTTAGTGGGATAAGTAATGGAA
1 TTTTACTGGAATAAGTAATGGAA
1129059 CTTGGAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (25 bp):
TTTTACTGGAATAAGTAATGGAAGC
Found at i:1134109 original size:26 final size:26
Alignment explanation
Indices: 1134080--1134131 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1134070 AATAAAAGAA
1134080 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTTAATTAG
1134106 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTTTAATTAG
1134132 CATTAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTTAATTAG
Found at i:1138438 original size:75 final size:75
Alignment explanation
Indices: 1138313--1138461 Score: 264
Period size: 75 Copynumber: 2.0 Consensus size: 75
1138303 TAGCTTTTGA
* *
1138313 AACGACCTACACCTTTAGGTTTCCTTTTGGTTCTCCCATTAGCTTGGGTTGAACCACCTTAGTTT
1 AACGACCTACACCTTTAGGTTTCCTTTTGGTTCTCCAATTAGCTTCGGTTGAACCACCTTAGTTT
1138378 ATGGGCTATT
66 ATGGGCTATT
1138388 AACGACCTACACCTTTAGGTTTCCTTTTGGTTCTCCAATT-GCTTTCGGTTGAACCACCTTAGTT
1 AACGACCTACACCTTTAGGTTTCCTTTTGGTTCTCCAATTAGC-TTCGGTTGAACCACCTTAGTT
1138452 TATGGGCTAT
65 TATGGGCTAT
1138462 AATTATTGCA
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
74 2 0.03
75 69 0.97
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (75 bp):
AACGACCTACACCTTTAGGTTTCCTTTTGGTTCTCCAATTAGCTTCGGTTGAACCACCTTAGTTT
ATGGGCTATT
Found at i:1138489 original size:12 final size:13
Alignment explanation
Indices: 1138464--1138493 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1138454 TGGGCTATAA
1138464 TTATTGCATTTAT
1 TTATTGCATTTAT
1138477 TTATTGC-TTTAT
1 TTATTGCATTTAT
1138489 TTATT
1 TTATT
1138494 CATGTATGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (13 bp):
TTATTGCATTTAT
Found at i:1140034 original size:533 final size:534
Alignment explanation
Indices: 1139017--1140083 Score: 2109
Period size: 533 Copynumber: 2.0 Consensus size: 534
1139007 GAAATACTTT
1139017 CGAGAAAGTCTTTCTGAAATTAATATATGAGGGTTATTAATTTTGAAATAAAATAGTGGGAACAT
1 CGAGAAAGTCTTTCTGAAATTAATATATGAGGGTTATTAATTTTGAAATAAAATAGTGGGAACAT
1139082 CTTTTCATAAAGTCCTATTAATGATTGATATAAACTTGGTAAATTTACTCACACACATATTTTAT
66 CTTTTCATAAAGTCCTATTAATGATTGATATAAACTTGGTAAATTTACTCACACACATATTTTAT
1139147 AGTTGTAGATATGGCTGAAAACACTAATACACTCTCATTGCGATCGGTCCTTAAGAAGGACAAAT
131 AGTTGTAGATATGGCTGAAAACACTAATACACTCTCATTGCGATCGGTCCTTAAGAAGGACAAAT
*
1139212 TGAATGGTTTGAACTTTATTGACTGCTTTTGTAACTTAAGGATTGTTCTCAAACAAGAACGGAAA
196 TGAATGGTTTGAACTTTATTGACTGCTTTCGTAACTTAAGGATTGTTCTCAAACAAGAACGGAAA
1139277 TTATATGTCGTTGAACAACCAATTCCTAATGAACCACCCGCTAATGCCTCGAGGGTTGATAAAGA
261 TTATATGTCGTTGAACAACCAATTCCTAATGAACCACCCGCTAATGCCTCGAGGGTTGATAAAGA
1139342 TTCTTACAAGAAGCATCCCGATGACATGGTAGACGTTGGATGTCTTATGCTTGCCACTATGAATC
326 TTCTTACAAGAAGCATCCCGATGACATGGTAGACGTTGGATGTCTTATGCTTGCCACTATGAATC
1139407 TTAAGCTTCAAAAGCAACATGAGGACATGGTTGCTTATGATATGAACGAGCACCTAAAAGAACTT
391 TTAAGCTTCAAAAGCAACATGAGGACATGGTTGCTTATGATATGAACGAGCACCTAAAAGAACTT
1139472 TATCAAGGGTAAGCATGGCAAGAGAGGTTTGATACCTCTAAAGCCCTATTCCAATGTAAGCTAGC
456 TATCAAGGGTAAGCATGGCAAGAGAGGTTTGATACCTCTAAAGCCCTATTCCAATGTAAGCTAGC
1139537 TGAAGGAAGCCCAG
521 TGAAGGAAGCCCAG
1139551 CGAGAAAGTC-TTCTGAAATTAATATATGAGGGTTATTAATTTTGAAATAAAATAGTGGGAACAT
1 CGAGAAAGTCTTTCTGAAATTAATATATGAGGGTTATTAATTTTGAAATAAAATAGTGGGAACAT
1139615 CTTTTCATAAAGTCCTATTAATGATTGATATAAACTTGGTAAATTTACTCACACACATATTTTAT
66 CTTTTCATAAAGTCCTATTAATGATTGATATAAACTTGGTAAATTTACTCACACACATATTTTAT
1139680 AGTTGTAGATATGGCTGAAAACACTAATACACTCTCATTGCGATCGGTCCTTAAGAAGGACAAAT
131 AGTTGTAGATATGGCTGAAAACACTAATACACTCTCATTGCGATCGGTCCTTAAGAAGGACAAAT
*
1139745 TGAATGGTTTGAACTTTATTGACTGGTTTCGTAACTTAAGGATTGTTCTCAAACAAGAACGGAAA
196 TGAATGGTTTGAACTTTATTGACTGCTTTCGTAACTTAAGGATTGTTCTCAAACAAGAACGGAAA
1139810 TTATATGTCGTTGAACAACCAATTCCTAATGAACCACCCGCTAATGCCTCGAGGGTTGATAAAGA
261 TTATATGTCGTTGAACAACCAATTCCTAATGAACCACCCGCTAATGCCTCGAGGGTTGATAAAGA
1139875 TTCTTACAAGAAGCATCCCGATGACATGGTAGACGTTGGATGTCTTATGCTTGCCACTATGAATC
326 TTCTTACAAGAAGCATCCCGATGACATGGTAGACGTTGGATGTCTTATGCTTGCCACTATGAATC
1139940 TTAAGCTTCAAAAGCAACATGAGGACATGGTTGCTTATGATATGAACGAGCACCTAAAAGAACTT
391 TTAAGCTTCAAAAGCAACATGAGGACATGGTTGCTTATGATATGAACGAGCACCTAAAAGAACTT
1140005 TATCAAGGGTAAGCATGGCAAGAGAGGTTTGATACCTCTAAAGCCCTATTCCAATGTAAGCTAGC
456 TATCAAGGGTAAGCATGGCAAGAGAGGTTTGATACCTCTAAAGCCCTATTCCAATGTAAGCTAGC
1140070 TGAAGGAAGCCCAG
521 TGAAGGAAGCCCAG
1140084 TATGACCTCA
Statistics
Matches: 531, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
533 521 0.98
534 10 0.02
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (534 bp):
CGAGAAAGTCTTTCTGAAATTAATATATGAGGGTTATTAATTTTGAAATAAAATAGTGGGAACAT
CTTTTCATAAAGTCCTATTAATGATTGATATAAACTTGGTAAATTTACTCACACACATATTTTAT
AGTTGTAGATATGGCTGAAAACACTAATACACTCTCATTGCGATCGGTCCTTAAGAAGGACAAAT
TGAATGGTTTGAACTTTATTGACTGCTTTCGTAACTTAAGGATTGTTCTCAAACAAGAACGGAAA
TTATATGTCGTTGAACAACCAATTCCTAATGAACCACCCGCTAATGCCTCGAGGGTTGATAAAGA
TTCTTACAAGAAGCATCCCGATGACATGGTAGACGTTGGATGTCTTATGCTTGCCACTATGAATC
TTAAGCTTCAAAAGCAACATGAGGACATGGTTGCTTATGATATGAACGAGCACCTAAAAGAACTT
TATCAAGGGTAAGCATGGCAAGAGAGGTTTGATACCTCTAAAGCCCTATTCCAATGTAAGCTAGC
TGAAGGAAGCCCAG
Found at i:1152322 original size:24 final size:25
Alignment explanation
Indices: 1152294--1152341 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
1152284 TCTGACCCAA
*
1152294 TTTTACTGGAATATG-AATGGAACC
1 TTTTACTGGAATAAGTAATGGAACC
* *
1152318 TTTTAGTGGGATAAGTAATGGAAC
1 TTTTACTGGAATAAGTAATGGAAC
1152342 TTGGAAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.33
Consensus pattern (25 bp):
TTTTACTGGAATAAGTAATGGAACC
Found at i:1154404 original size:24 final size:25
Alignment explanation
Indices: 1154376--1154422 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
1154366 TCCGACCCAA
*
1154376 TTTTACTGGAATATG-AATGGAAGC
1 TTTTACTGGAATAAGTAATGGAAGC
* *
1154400 TTTTAGTGGGATAAGTAATGGAA
1 TTTTACTGGAATAAGTAATGGAA
1154423 CTTGGAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (25 bp):
TTTTACTGGAATAAGTAATGGAAGC
Done.