Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold165.1
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: 1724686
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 30232 characters in sequence are not A, C, G, or T
File 6 of 8
Found at i:1171951 original size:19 final size:20
Alignment explanation
Indices: 1171924--1171964 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
1171914 AAAATTTTAA
1171924 TTAAATAAT-TATTAAAA-TT
1 TTAAATAATAT-TTAAAAGTT
*
1171943 TTAAGTAATATTTAAAAGTT
1 TTAAATAATATTTAAAAGTT
1171963 TT
1 TT
1171965 TGATAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTAAATAATATTTAAAAGTT
Found at i:1172706 original size:8 final size:7
Alignment explanation
Indices: 1172686--1172777 Score: 76
Period size: 7 Copynumber: 12.3 Consensus size: 7
1172676 ACCCTTGACA
1172686 CCCTAAC
1 CCCTAAC
*
1172693 CCCTAAAT
1 CCCT-AAC
1172701 CCCTAAC
1 CCCTAAC
1172708 CCCTAAC
1 CCCTAAC
1172715 CCCTAAATCC
1 CCCT-AA--C
1172725 CCCTAAC
1 CCCTAAC
* *
1172732 TCCTAAAT
1 CCCT-AAC
*
1172740 CACTAAC
1 CCCTAAC
1172747 CCCTAAC
1 CCCTAAC
*
1172754 CCCTAAAT
1 CCCT-AAC
*
1172762 TCCTAAC
1 CCCTAAC
1172769 CCCTAAC
1 CCCTAAC
1172776 CC
1 CC
1172778 TTAAACCTTA
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
7 43 0.64
8 17 0.25
9 2 0.03
10 5 0.07
ACGTcount: A:0.32, C:0.49, G:0.00, T:0.20
Consensus pattern (7 bp):
CCCTAAC
Found at i:1172714 original size:22 final size:22
Alignment explanation
Indices: 1172686--1172782 Score: 123
Period size: 22 Copynumber: 4.6 Consensus size: 22
1172676 ACCCTTGACA
1172686 CCCTAACCCCTAAATCCCTAAC
1 CCCTAACCCCTAAATCCCTAAC
1172708 CCCTAACCCCTAAAT--C---C
1 CCCTAACCCCTAAATCCCTAAC
* *
1172725 CCCTAACTCCTAAATCACTAAC
1 CCCTAACCCCTAAATCCCTAAC
*
1172747 CCCTAACCCCTAAATTCCTAAC
1 CCCTAACCCCTAAATCCCTAAC
*
1172769 CCCTAACCCTTAAA
1 CCCTAACCCCTAAA
1172783 CCTTAATCCC
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
17 15 0.23
19 1 0.02
20 1 0.02
22 48 0.74
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.21
Consensus pattern (22 bp):
CCCTAACCCCTAAATCCCTAAC
Found at i:1172729 original size:17 final size:16
Alignment explanation
Indices: 1172707--1172752 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
1172697 AAATCCCTAA
1172707 CCCCTAACCCCTAAAT
1 CCCCTAACCCCTAAAT
*
1172723 CCCCCTAACTCCTAAAT
1 -CCCCTAACCCCTAAAT
*
1172740 -CACTAACCCCTAA
1 CCCCTAACCCCTAA
1172753 CCCCTAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 11 0.42
17 15 0.58
ACGTcount: A:0.33, C:0.48, G:0.00, T:0.20
Consensus pattern (16 bp):
CCCCTAACCCCTAAAT
Found at i:1172731 original size:39 final size:37
Alignment explanation
Indices: 1172686--1172774 Score: 133
Period size: 39 Copynumber: 2.4 Consensus size: 37
1172676 ACCCTTGACA
*
1172686 CCCTAACCCCTAAATCCCTAACCCCTAACCCCTAAAT
1 CCCTAACCCCTAAATCACTAACCCCTAACCCCTAAAT
*
1172723 CCCCCTAACTCCTAAATCACTAACCCCTAACCCCTAAAT
1 --CCCTAACCCCTAAATCACTAACCCCTAACCCCTAAAT
*
1172762 TCCTAACCCCTAA
1 CCCTAACCCCTAA
1172775 CCCTTAAACC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
37 11 0.24
39 35 0.76
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.20
Consensus pattern (37 bp):
CCCTAACCCCTAAATCACTAACCCCTAACCCCTAAAT
Found at i:1172784 original size:15 final size:14
Alignment explanation
Indices: 1172685--1172784 Score: 55
Period size: 15 Copynumber: 6.7 Consensus size: 14
1172675 TACCCTTGAC
1172685 ACCCT-AACCCCTAA
1 ACCCTAAACCCCT-A
1172699 ATCCCT-AACCCCTA
1 A-CCCTAAACCCCTA
1172713 ACCCCTAAATCCCCCTA
1 A-CCCTAAA--CCCCTA
* *
1172730 ACTCCTAAATCACTA
1 AC-CCTAAACCCCTA
1172745 ACCCCT-AACCCCTAA
1 A-CCCTAAACCCCT-A
*
1172760 ATTCCT-AACCCCTA
1 A-CCCTAAACCCCTA
1172774 ACCCTTAAACC
1 ACCC-TAAACC
1172785 TTAATCCCAA
Statistics
Matches: 69, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
13 2 0.03
14 15 0.22
15 37 0.54
16 2 0.03
17 13 0.19
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.20
Consensus pattern (14 bp):
ACCCTAAACCCCTA
Found at i:1173472 original size:41 final size:40
Alignment explanation
Indices: 1173404--1173562 Score: 140
Period size: 41 Copynumber: 3.9 Consensus size: 40
1173394 CTAAAACTCC
*
1173404 AACATTAGCGGCGCTT-TACAAACAAACGCCACTAAAAACCTT
1 AACATTAGCGGCGCTTGT--AAA-AAACGCCACTAAAAACCAT
* * * * * *
1173446 AACTTTGGCGGCGCATTGTCAAAAACGCCGCTAAAAGCCCT
1 AACATTAGCGGCGC-TTGTAAAAAACGCCACTAAAAACCAT
* * *
1173487 AAAATTAGCGGCGCTCAGGAAAAAACGCCACTAAAAACCAT
1 AACATTAGCGGCGCT-TGTAAAAAACGCCACTAAAAACCAT
* * *
1173528 AACATTAGCGGTGTTTGTTTAAAAACGCCACTAAA
1 AACATTAGCGGCGCTTG-TAAAAAACGCCACTAAA
1173563 GCCCTCTTAA
Statistics
Matches: 92, Mismatches: 21, Indels: 9
0.75 0.17 0.07
Matches are distributed among these distances:
40 2 0.02
41 73 0.79
42 14 0.15
43 2 0.02
44 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (40 bp):
AACATTAGCGGCGCTTGTAAAAAACGCCACTAAAAACCAT
Found at i:1173562 original size:82 final size:83
Alignment explanation
Indices: 1173385--1173538 Score: 208
Period size: 82 Copynumber: 1.9 Consensus size: 83
1173375 CGTTTCCATC
* * *
1173385 AAAACGCCGCTAAAA-CTCC-AACATTAGCGGCGCTTTACAAACAAACGCCACTAAAAACCTTAA
1 AAAACGCCGCTAAAAGC-CCTAAAATTAGCGGCGCTTCACAAACAAACGCCACTAAAAACCATAA
* *
1173448 CTTTGGCGGCGCATTGTCA
65 CATTAGCGGCGCATTGTCA
*
1173467 AAAACGCCGCTAAAAGCCCTAAAATTAGCGGCGC-TCAGGAAA-AAACGCCACTAAAAACCATAA
1 AAAACGCCGCTAAAAGCCCTAAAATTAGCGGCGCTTCA-CAAACAAACGCCACTAAAAACCATAA
1173530 CATTAGCGG
65 CATTAGCGG
1173539 TGTTTGTTTA
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
82 46 0.73
83 17 0.27
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.16
Consensus pattern (83 bp):
AAAACGCCGCTAAAAGCCCTAAAATTAGCGGCGCTTCACAAACAAACGCCACTAAAAACCATAAC
ATTAGCGGCGCATTGTCA
Found at i:1177719 original size:14 final size:14
Alignment explanation
Indices: 1177692--1177728 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1177682 AAAACCCTAA
1177692 TTTT-TTTC-CTCT
1 TTTTCTTTCTCTCT
1177704 TTTTCTTTCTCTCT
1 TTTTCTTTCTCTCT
1177718 TTTTC-TTCTCT
1 TTTTCTTTCTCT
1177729 GTTTCGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 10 0.43
14 9 0.39
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTCTTTCTCTCT
Found at i:1178525 original size:19 final size:19
Alignment explanation
Indices: 1178497--1178545 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
1178487 TATTATTTAT
1178497 ATTTTATTTAAAAAAATATA
1 ATTTT-TTTAAAAAAATATA
1178517 ATTTTTTT-AAAAAATATA
1 ATTTTTTTAAAAAAATATA
* *
1178535 AATTTTATAAA
1 ATTTTTTTAAA
1178546 TATTTTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 16 0.62
19 5 0.19
20 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTTTTTAAAAAAATATA
Found at i:1178583 original size:20 final size:19
Alignment explanation
Indices: 1178535--1178591 Score: 80
Period size: 20 Copynumber: 3.0 Consensus size: 19
1178525 AAAAAATATA
*
1178535 AATTTTATAAA-TATTTTG
1 AATTTTAAAAATTATTTTG
1178553 AATTTTAAAAATTATTTTG
1 AATTTTAAAAATTATTTTG
*
1178572 AATTTTTGAAAATTATTTTG
1 AA-TTTTAAAAATTATTTTG
1178592 TTTTTGTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.29
19 9 0.26
20 16 0.46
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (19 bp):
AATTTTAAAAATTATTTTG
Found at i:1180290 original size:46 final size:46
Alignment explanation
Indices: 1180187--1180492 Score: 465
Period size: 46 Copynumber: 6.6 Consensus size: 46
1180177 TACGTATGAT
* *
1180187 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1180230 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
1180276 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
1180322 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* ** *
1180368 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1180414 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1180466 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
1180493 AGTACTCAAA
Statistics
Matches: 244, Mismatches: 10, Indels: 15
0.91 0.04 0.06
Matches are distributed among these distances:
43 10 0.04
44 5 0.02
45 20 0.08
46 166 0.68
49 2 0.01
52 41 0.17
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:1181525 original size:16 final size:17
Alignment explanation
Indices: 1181493--1181525 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1181483 CAATTAACCC
1181493 CTCAATTAATCTAATTTT
1 CTCAATTAA-CTAATTTT
1181511 CTCAATTAA-TAATTT
1 CTCAATTAACTAATTT
1181526 ACCTAGACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
CTCAATTAACTAATTTT
Found at i:1181978 original size:17 final size:17
Alignment explanation
Indices: 1181952--1181995 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
1181942 TGGTCCTAAC
*
1181952 TTTATTATTTAAGCTAT
1 TTTATCATTTAAGCTAT
1181969 TTTATCATTTAAGCTAT
1 TTTATCATTTAAGCTAT
1181986 TTTATCATTT
1 TTTATCATTT
1181996 CCCATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.27, C:0.09, G:0.05, T:0.59
Consensus pattern (17 bp):
TTTATCATTTAAGCTAT
Found at i:1183551 original size:31 final size:29
Alignment explanation
Indices: 1183513--1183585 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 29
1183503 TATGTGTTAT
*
1183513 ATTTTTATAATTAAAAAAATTTACGTATTAC
1 ATTTTTATAATTAAAAAAATGT--GTATTAC
* *
1183544 GTTTTTATAA-T-AAAAAATGTGTATTGC
1 ATTTTTATAATTAAAAAAATGTGTATTAC
1183571 ATTTTTATAATTAAA
1 ATTTTTATAATTAAA
1183586 TATATGTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 15 0.42
28 1 0.03
29 10 0.28
30 1 0.03
31 9 0.25
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (29 bp):
ATTTTTATAATTAAAAAAATGTGTATTAC
Found at i:1183567 original size:27 final size:27
Alignment explanation
Indices: 1183496--1183595 Score: 83
Period size: 27 Copynumber: 3.6 Consensus size: 27
1183486 ATTTAGTGCT
* * *
1183496 TAAAAAGTATGTGTTATATTTTTATAA
1 TAAAAAATATGTATTACATTTTTATAA
* *
1183523 TTAAAAAAATTTACGTATTACGTTTTTATAA
1 -T-AAAAAA--TATGTATTACATTTTTATAA
* *
1183554 TAAAAAATGTGTATTGCATTTTTATAA
1 TAAAAAATATGTATTACATTTTTATAA
* *
1183581 TTAAATATATGTATT
1 TAAAAAATATGTATT
1183596 TAAAAAATAT
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
27 28 0.49
28 1 0.02
29 11 0.19
30 1 0.02
31 16 0.28
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (27 bp):
TAAAAAATATGTATTACATTTTTATAA
Found at i:1186076 original size:27 final size:27
Alignment explanation
Indices: 1186046--1186101 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
1186036 TATTTAGTGC
* *
1186046 TTAAAAATATGTGTTATATTTTTATAA
1 TTAAAAATACGTGTTACATTTTTATAA
* * *
1186073 TTAAAAGTGCGTGTTGCATTTTTATAA
1 TTAAAAATACGTGTTACATTTTTATAA
1186100 TT
1 TT
1186102 GAATATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.12, T:0.50
Consensus pattern (27 bp):
TTAAAAATACGTGTTACATTTTTATAA
Found at i:1186579 original size:42 final size:42
Alignment explanation
Indices: 1186532--1186819 Score: 265
Period size: 42 Copynumber: 6.8 Consensus size: 42
1186522 CAAACAAAAA
*
1186532 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTGAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* **
1186574 CGCCGCTAAAGAACATTATCTTTAGCAACGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* * *
1186616 CGCCGCTAAAGAATATGATCTTTAGTGGCGTTTTTTAT-TAGG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT-TCTAAG
* * * * * *
1186658 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGTATATG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* * * * * *** *
1186700 CGCCGCTAAAGAACATGTTCTTTAACAGCGCTTTGTAAAAAA
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* * * * *
1186742 CGCCGCTAGAGATCATAATCTTTCGCGGCGCTTTTTTTAC-AAA
1 CGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTT-CTAAG
* * *
1186785 CGCCACTAAAGAACATGTTCTTTAGCGGCGCTTTT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
1186820 GTACAAAAAC
Statistics
Matches: 196, Mismatches: 46, Indels: 8
0.78 0.18 0.03
Matches are distributed among these distances:
41 1 0.01
42 163 0.83
43 32 0.16
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.33
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
Found at i:1186763 original size:126 final size:126
Alignment explanation
Indices: 1186529--1186822 Score: 310
Period size: 126 Copynumber: 2.3 Consensus size: 126
1186519 TTCCAAACAA
* * *
1186529 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTGAGCGCCGCTAAAGAACATTATC
1 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTGTATGAGCGCCGCTAAAGAACATTATC
* * * *** * * * *
1186594 TTTAGCAACGTTTTTTTCTAAGCGCCGCTAAAGAATATGATCTTTAGTGGCG--TTTTTTATT
65 TTTAACAACGCTTTGTAAAAAACGCCGCTAAAGAATATAATCTTTAGCGGCGCTTTTTTTA-C
** *
1186655 AGGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGTAT-ATGCGCCGCTAAAGAACATGT-
1 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTT-TGTATGA-GCGCCGCTAAAGAACAT-TA
* * *
1186718 TCTTTAACAGCGCTTTGTAAAAAACGCCGCTAGAG-ATCATAATCTTTCGCGGCGCTTTTTTTAC
63 TCTTTAACAACGCTTTGTAAAAAACGCCGCTAAAGAAT-ATAATCTTTAGCGGCGCTTTTTTTAC
*
1186782 AAACGCCACTAAAGAACATGTTCTTTAGCGGCGCTTTTGTA
1 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTGTA
1186823 CAAAAACGCC
Statistics
Matches: 138, Mismatches: 23, Indels: 13
0.79 0.13 0.07
Matches are distributed among these distances:
125 6 0.04
126 88 0.64
127 34 0.25
128 10 0.07
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (126 bp):
AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTGTATGAGCGCCGCTAAAGAACATTATCT
TTAACAACGCTTTGTAAAAAACGCCGCTAAAGAATATAATCTTTAGCGGCGCTTTTTTTAC
Found at i:1192859 original size:9 final size:9
Alignment explanation
Indices: 1192845--1192925 Score: 60
Period size: 9 Copynumber: 9.0 Consensus size: 9
1192835 TAAATATTAA
1192845 TAAGTTATG
1 TAAGTTATG
1192854 TAAGTTATG
1 TAAGTTATG
* *
1192863 TATTA-TAAATT
1 TA--AGT-TATG
*
1192874 TAAATTATG
1 TAAGTTATG
1192883 TAAGTTATG
1 TAAGTTATG
1192892 -AA-TTATG
1 TAAGTTATG
1192899 TAAGTTATG
1 TAAGTTATG
* *
1192908 TAAATTACG
1 TAAGTTATG
*
1192917 TGAGTTATG
1 TAAGTTATG
1192926 AAATTTGAAC
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
7 5 0.09
8 4 0.07
9 40 0.71
10 2 0.04
11 5 0.09
ACGTcount: A:0.37, C:0.01, G:0.17, T:0.44
Consensus pattern (9 bp):
TAAGTTATG
Found at i:1192897 original size:16 final size:16
Alignment explanation
Indices: 1192849--1192927 Score: 74
Period size: 16 Copynumber: 5.0 Consensus size: 16
1192839 TATTAATAAG
*
1192849 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGAA
* *
1192865 TTA--TAAATT-TAAA
1 TTATGTAAGTTATGAA
1192878 TTATGTAAGTTATGAA
1 TTATGTAAGTTATGAA
1192894 TTATGTAAGTTATGTAAA
1 TTATGTAAGTTATG--AA
* *
1192912 TTACGTGAGTTATGAA
1 TTATGTAAGTTATGAA
1192928 ATTTGAACTT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
13 5 0.10
14 5 0.10
15 5 0.10
16 22 0.43
18 14 0.27
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.44
Consensus pattern (16 bp):
TTATGTAAGTTATGAA
Found at i:1193000 original size:34 final size:35
Alignment explanation
Indices: 1192942--1193021 Score: 135
Period size: 34 Copynumber: 2.3 Consensus size: 35
1192932 GAACTTTAAA
* *
1192942 AAAATTAAATATTTAAAAATATTCGTGATTAAAAT
1 AAAATAAAATATTTAAAAAAATTCGTGATTAAAAT
1192977 AAAATAAAATA-TTAAAAAAATTCGTGATTAAAAT
1 AAAATAAAATATTTAAAAAAATTCGTGATTAAAAT
1193011 AAAATAAAATA
1 AAAATAAAATA
1193022 AAATATTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
34 33 0.77
35 10 0.23
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (35 bp):
AAAATAAAATATTTAAAAAAATTCGTGATTAAAAT
Found at i:1194722 original size:44 final size:44
Alignment explanation
Indices: 1194659--1194745 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
1194649 TGGAAGGAGA
1194659 AAGGAGGCGATTTAGGGATTTGGGATTTCAAGAAATTCGGCAAG
1 AAGGAGGCGATTTAGGGATTTGGGATTTCAAGAAATTCGGCAAG
* *
1194703 AAGGAGGCGATTTATGGATTTGGGATTTCAAGAAATTGGGCAA
1 AAGGAGGCGATTTAGGGATTTGGGATTTCAAGAAATTCGGCAA
1194746 AAAGATTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.32, C:0.08, G:0.33, T:0.26
Consensus pattern (44 bp):
AAGGAGGCGATTTAGGGATTTGGGATTTCAAGAAATTCGGCAAG
Found at i:1203709 original size:9 final size:9
Alignment explanation
Indices: 1203669--1204237 Score: 237
Period size: 9 Copynumber: 67.2 Consensus size: 9
1203659 AAGTTATTTA
1203669 TTATGTAAG
1 TTATGTAAG
*
1203678 TTAT-TTA-
1 TTATGTAAG
*
1203685 TTATATAAG
1 TTATGTAAG
1203694 TTATGTAAG
1 TTATGTAAG
*
1203703 TTGTGTAAG
1 TTATGTAAG
*
1203712 TTGTGT-A-
1 TTATGTAAG
* *
1203719 TTATGAAAC
1 TTATGTAAG
1203728 TTATGTAAG
1 TTATGTAAG
*
1203737 TTATGT--C
1 TTATGTAAG
1203744 TTATGTAAG
1 TTATGTAAG
*
1203753 TTATGTAAA
1 TTATGTAAG
1203762 TTATGT-A-
1 TTATGTAAG
1203769 TTATGTAAG
1 TTATGTAAG
1203778 TTATGTAAG
1 TTATGTAAG
*
1203787 TTGTGT-A-
1 TTATGTAAG
1203794 TTATGTAAG
1 TTATGTAAG
1203803 TTATGTAAG
1 TTATGTAAG
*
1203812 TTGTGT-A-
1 TTATGTAAG
1203819 TTATGTAAG
1 TTATGTAAG
1203828 TTATGTAAG
1 TTATGTAAG
*
1203837 TTGTGT-A-
1 TTATGTAAG
*
1203844 TTATTTACA-
1 TTATGTA-AG
*
1203853 -CATGTAAG
1 TTATGTAAG
*
1203861 TTGTGT-A-
1 TTATGTAAG
1203868 TTATGTAAG
1 TTATGTAAG
1203877 TTATGT-A-
1 TTATGTAAG
*
1203884 TTATTTACA-
1 TTATGTA-AG
*
1203893 -CATGTAAG
1 TTATGTAAG
*
1203901 TTGTGT-A-
1 TTATGTAAG
1203908 TTATGTAAG
1 TTATGTAAG
1203917 TTATGTAAG
1 TTATGTAAG
1203926 TTATGT-A-
1 TTATGTAAG
* *
1203933 TTAAGTAGG
1 TTATGTAAG
1203942 TTATGTAAG
1 TTATGTAAG
1203951 TTATGT-A-
1 TTATGTAAG
1203958 TTATGTAAG
1 TTATGTAAG
1203967 TTATGTAAG
1 TTATGTAAG
* **
1203976 TTTTTGT-TT
1 -TTATGTAAG
*
1203985 TTGTGT-A-
1 TTATGTAAG
*
1203992 TTATGTAAC
1 TTATGTAAG
* *
1204001 TTATTTAAT
1 TTATGTAAG
*
1204010 TTATGTATG
1 TTATGTAAG
*
1204019 GTATGTATTA-
1 TTATGTA--AG
1204029 TTATGTAAG
1 TTATGTAAG
*
1204038 TTAT-TATG
1 TTATGTAAG
*
1204046 -TA-GGATA-
1 TTATGTA-AG
1204053 TTATGTAAG
1 TTATGTAAG
1204062 TTATGTAAG
1 TTATGTAAG
* **
1204071 TTTTTGT-TT
1 -TTATGTAAG
*
1204080 TTGTGT-A-
1 TTATGTAAG
*
1204087 TTATGTAAC
1 TTATGTAAG
* *
1204096 TTATTTAAT
1 TTATGTAAG
*
1204105 TTATGTATGG
1 TTATGTA-AG
* *
1204115 TATATATTA-
1 T-TATGTAAG
1204124 TTATGTAAG
1 TTATGTAAG
1204133 TTATGTAAG
1 TTATGTAAG
* **
1204142 TTTTTGT-TT
1 -TTATGTAAG
*
1204151 TTGTGT-A-
1 TTATGTAAG
*
1204158 TTATGTAAC
1 TTATGTAAG
* *
1204167 TTATTTAAT
1 TTATGTAAG
1204176 TTATGTAAG
1 TTATGTAAG
1204185 -TATGTATTA-
1 TTATGTA--AG
1204194 TTATGTAAG
1 TTATGTAAG
*
1204203 TTAT-TATG
1 TTATGTAAG
*
1204211 -TA-GGATA-
1 TTATGTA-AG
1204218 TTATGTAAG
1 TTATGTAAG
1204227 TTATGTAAG
1 TTATGTAAG
1204236 TT
1 TT
1204238 TTTGTTTTTG
Statistics
Matches: 422, Mismatches: 81, Indels: 114
0.68 0.13 0.18
Matches are distributed among these distances:
7 83 0.20
8 72 0.17
9 234 0.55
10 29 0.07
11 4 0.01
ACGTcount: A:0.29, C:0.02, G:0.19, T:0.51
Consensus pattern (9 bp):
TTATGTAAG
Found at i:1203722 original size:25 final size:25
Alignment explanation
Indices: 1203694--1203883 Score: 276
Period size: 25 Copynumber: 7.6 Consensus size: 25
1203684 ATTATATAAG
*
1203694 TTATGTAAGTTGTGTAAGTTGTGTA
1 TTATGTAAGTTATGTAAGTTGTGTA
* * * *
1203719 TTATGAAACTTATGTAAGTTATGTC
1 TTATGTAAGTTATGTAAGTTGTGTA
* *
1203744 TTATGTAAGTTATGTAAATTATGTA
1 TTATGTAAGTTATGTAAGTTGTGTA
1203769 TTATGTAAGTTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTAAGTTGTGTA
1203794 TTATGTAAGTTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTAAGTTGTGTA
1203819 TTATGTAAGTTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTAAGTTGTGTA
* *
1203844 TTATTTACA--CATGTAAGTTGTGTA
1 TTATGTA-AGTTATGTAAGTTGTGTA
1203868 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
1203884 TTATTTACAC
Statistics
Matches: 147, Mismatches: 15, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
23 1 0.01
24 20 0.14
25 125 0.85
26 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.21, T:0.47
Consensus pattern (25 bp):
TTATGTAAGTTATGTAAGTTGTGTA
Found at i:1203884 original size:40 final size:40
Alignment explanation
Indices: 1203828--1203923 Score: 183
Period size: 40 Copynumber: 2.4 Consensus size: 40
1203818 ATTATGTAAG
*
1203828 TTATGTAAGTTGTGTATTATTTACACATGTAAGTTGTGTA
1 TTATGTAAGTTATGTATTATTTACACATGTAAGTTGTGTA
1203868 TTATGTAAGTTATGTATTATTTACACATGTAAGTTGTGTA
1 TTATGTAAGTTATGTATTATTTACACATGTAAGTTGTGTA
1203908 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
1203924 AGTTATGTAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.29, C:0.04, G:0.19, T:0.48
Consensus pattern (40 bp):
TTATGTAAGTTATGTATTATTTACACATGTAAGTTGTGTA
Found at i:1203926 original size:25 final size:25
Alignment explanation
Indices: 1203669--1204068 Score: 126
Period size: 25 Copynumber: 15.6 Consensus size: 25
1203659 AAGTTATTTA
* *
1203669 TTATGTAAGTTATTTATTATATAAG
1 TTATGTAAGTTATGTATTATGTAAG
* *
1203694 TTATGTAAGTTGTGTAAGTTGTGT-A-
1 TTATGTAAGTTATGT-A-TTATGTAAG
* * *
1203719 TTATGAAACTTATGTAAGTTATGT--C
1 TTATGTAAGTTATGT-A-TTATGTAAG
1203744 TTATGTAAGTTATGTAAATTATGT-A-
1 TTATGTAAGTTATGT--ATTATGTAAG
*
1203769 TTATGTAAGTTATGTAAGTTGTGT-A-
1 TTATGTAAGTTATGT-A-TTATGTAAG
*
1203794 TTATGTAAGTTATGTAAGTTGTGT-A-
1 TTATGTAAGTTATGT-A-TTATGTAAG
* *
1203819 TTATGTAAGTTATGTAAGTTGTGTATTAT
1 TTATGTAAGTTATGT-A-TTATGTA--AG
*
1203848 TTACACATGTAAGTTGTGTATTATGTAAG
1 TT----ATGTAAGTTATGTATTATGTAAG
* **
1203877 TTATGT-A-TTATTTACACATGTAAG
1 TTATGTAAGTTATGTA-TTATGTAAG
*
1203901 TTGTGT-A-TTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGT-A-TTATGTAAG
*
1203926 TTATGT-A-TTAAGTAGGTTATGTAAG
1 TTATGTAAGTTATGTA--TTATGTAAG
1203951 TTATGT-A-TTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGT-A-TTATGTAAG
* ** * *
1203976 TTTTTGT-TTTTGTGTATTATGTAAC
1 -TTATGTAAGTTATGTATTATGTAAG
* *
1204001 TTATTTAATTTATGTATGGTATGTATTA-
1 TTATGTAAGTTATGTAT--TATGTA--AG
*
1204029 TTATGTAAGTTAT-TATGTA-GGATA-
1 TTATGTAAGTTATGTAT-TATGTA-AG
1204053 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
1204069 AGTTTTTGTT
Statistics
Matches: 312, Mismatches: 37, Indels: 52
0.78 0.09 0.13
Matches are distributed among these distances:
23 5 0.02
24 41 0.13
25 197 0.63
26 14 0.04
27 18 0.06
28 12 0.04
29 6 0.02
31 6 0.02
32 1 0.00
33 12 0.04
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.49
Consensus pattern (25 bp):
TTATGTAAGTTATGTATTATGTAAG
Found at i:1203971 original size:16 final size:17
Alignment explanation
Indices: 1203658--1203973 Score: 205
Period size: 16 Copynumber: 18.6 Consensus size: 17
1203648 GATTTAGGAA
*
1203658 TAAGTTATTTA-TTATG
1 TAAGTTATGTAGTTATG
* *
1203674 TAAGTTATTTA-TTATA
1 TAAGTTATGTAGTTATG
*
1203690 TAAGTTATGTAAGTTGTG
1 TAAGTTATGT-AGTTATG
*
1203708 TAAGTTGTGTA-TTATG
1 TAAGTTATGTAGTTATG
* *
1203724 AAACTTATGTAAGTTATG
1 TAAGTTATGT-AGTTATG
*
1203742 T--CTTATGTAAGTTATG
1 TAAGTTATGT-AGTTATG
*
1203758 TAAATTATGTA-TTATG
1 TAAGTTATGTAGTTATG
*
1203774 TAAGTTATGTAAGTTGTG
1 TAAGTTATGT-AGTTATG
1203792 T-A-TTATGTAAGTTATG
1 TAAGTTATGT-AGTTATG
*
1203808 TAAGTTGTGTA-TTATG
1 TAAGTTATGTAGTTATG
*
1203824 TAAGTTATGTAAGTTGTG
1 TAAGTTATGT-AGTTATG
* ***
1203842 T-A-TTATTTACACATG
1 TAAGTTATGTAGTTATG
*
1203857 TAAGTTGTGTA-TTATG
1 TAAGTTATGTAGTTATG
*
1203873 TAAGTTATGTATTATTTACACATG
1 TAAGTTATG---TAGTT----ATG
*
1203897 TAAGTTGTGTA-TTATG
1 TAAGTTATGTAGTTATG
1203913 TAAGTTATGTAAGTTATG
1 TAAGTTATGT-AGTTATG
*
1203931 T-A-TTAAGTAGGTTATG
1 TAAGTTATGTA-GTTATG
1203947 TAAGTTATGTA-TTATG
1 TAAGTTATGTAGTTATG
1203963 TAAGTTATGTA
1 TAAGTTATGTA
1203974 AGTTTTTGTT
Statistics
Matches: 242, Mismatches: 31, Indels: 54
0.74 0.09 0.17
Matches are distributed among these distances:
15 5 0.02
16 150 0.62
17 18 0.07
18 50 0.21
19 2 0.01
20 4 0.02
21 2 0.01
24 11 0.05
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.48
Consensus pattern (17 bp):
TAAGTTATGTAGTTATG
Found at i:1204070 original size:95 final size:95
Alignment explanation
Indices: 1203956--1204136 Score: 353
Period size: 95 Copynumber: 1.9 Consensus size: 95
1203946 GTAAGTTATG
1203956 TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTATGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTATGGT
*
1204021 ATGTATTATTATGTAAGTTATTATGTAGGA
66 ATATATTATTATGTAAGTTATTATGTAGGA
1204051 TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTATGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTATGGT
1204116 ATATATTATTATGTAAGTTAT
66 ATATATTATTATGTAAGTTAT
1204137 GTAAGTTTTT
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 85 1.00
ACGTcount: A:0.28, C:0.01, G:0.17, T:0.55
Consensus pattern (95 bp):
TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTATGGT
ATATATTATTATGTAAGTTATTATGTAGGA
Found at i:1204111 original size:25 final size:25
Alignment explanation
Indices: 1204083--1204182 Score: 63
Period size: 25 Copynumber: 4.2 Consensus size: 25
1204073 TTTGTTTTTG
1204083 TGTATTATGTAACTTATTTAATTTA
1 TGTATTATGTAACTTATTTAATTTA
*
1204108 TGTA-T-GGT-A--TATATT-A-TTA
1 TGTATTATGTAACTTAT-TTAATTTA
* ** *
1204127 TGTAAGTTATGTAAGTT-TTTGTTTTTG
1 TGT-A-TTATGTAACTTATTT-AATTTA
1204154 TGTATTATGTAACTTATTTAATTTA
1 TGTATTATGTAACTTATTTAATTTA
1204179 TGTA
1 TGTA
1204183 AGTATGTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 24
0.63 0.09 0.28
Matches are distributed among these distances:
19 6 0.11
20 5 0.09
21 2 0.04
22 2 0.04
23 4 0.07
24 4 0.07
25 22 0.40
26 5 0.09
27 5 0.09
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (25 bp):
TGTATTATGTAACTTATTTAATTTA
Found at i:1204139 original size:71 final size:70
Alignment explanation
Indices: 1204051--1204206 Score: 285
Period size: 71 Copynumber: 2.2 Consensus size: 70
1204041 TTATGTAGGA
*
1204051 TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTATGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTA-AGT
1204116 ATATAT
65 ATATAT
1204122 TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTAAGTA
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTAAGTA
*
1204187 TGTAT
66 TATAT
1204192 TATTATGTAAGTTAT
1 TATTATGTAAGTTAT
1204207 TATGTAGGAT
Statistics
Matches: 83, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
70 22 0.27
71 61 0.73
ACGTcount: A:0.28, C:0.01, G:0.15, T:0.56
Consensus pattern (70 bp):
TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTAAGTA
TATAT
Found at i:1204231 original size:94 final size:95
Alignment explanation
Indices: 1204122--1204322 Score: 377
Period size: 94 Copynumber: 2.1 Consensus size: 95
1204112 TGGTATATAT
1204122 TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTA-AGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGAGT
1204186 ATGTATTATTATGTAAGTTATTATGTAGGA
66 ATGTATTATTATGTAAGTTATTATGTAGGA
*
1204216 TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGAGT
*
1204281 ATGTATTATTATGTAAGTTATTATGTAGGT
66 ATGTATTATTATGTAAGTTATTATGTAGGA
1204311 TATTATGTAAGT
1 TATTATGTAAGT
1204323 CATTATGTTG
Statistics
Matches: 104, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
94 61 0.59
95 43 0.41
ACGTcount: A:0.28, C:0.01, G:0.18, T:0.53
Consensus pattern (95 bp):
TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGAGT
ATGTATTATTATGTAAGTTATTATGTAGGA
Found at i:1204244 original size:165 final size:166
Alignment explanation
Indices: 1203956--1204301 Score: 658
Period size: 165 Copynumber: 2.1 Consensus size: 166
1203946 GTAAGTTATG
*
1203956 TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTATGGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTATAGT
1204021 ATGTATTATTATGTAAGTTATTATGTAGGATATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGT
66 ATGTATTATTATGTAAGTTATTATGTAGGATATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGT
*
1204086 ATTATGTAACTTATTTAATTTATGTATGGTATATAT
131 ATTATGTAACTTATTTAATTTATGTAGGGTATATAT
1204122 TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTA-AGT
1 TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTATAGT
1204186 ATGTATTATTATGTAAGTTATTATGTAGGATATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGT
66 ATGTATTATTATGTAAGTTATTATGTAGGATATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGT
*
1204251 ATTATGTAACTTATTTAATTTATGTAGGGTATGTAT
131 ATTATGTAACTTATTTAATTTATGTAGGGTATATAT
1204287 TATTATGTAAGTTAT
1 TATTATGTAAGTTAT
1204302 TATGTAGGTT
Statistics
Matches: 177, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
165 116 0.66
166 61 0.34
ACGTcount: A:0.27, C:0.01, G:0.17, T:0.54
Consensus pattern (166 bp):
TATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGTATTATGTAACTTATTTAATTTATGTATAGT
ATGTATTATTATGTAAGTTATTATGTAGGATATTATGTAAGTTATGTAAGTTTTTGTTTTTGTGT
ATTATGTAACTTATTTAATTTATGTAGGGTATATAT
Found at i:1204274 original size:43 final size:45
Alignment explanation
Indices: 1204152--1204294 Score: 146
Period size: 51 Copynumber: 3.1 Consensus size: 45
1204142 TTTTTGTTTT
1204152 TGTGTATTATGTAACTTATTTAATTTATGTAAGTATGTATTATTA
1 TGTGTATTATGTAACTTATTTAATTTATGTAAGTATGTATTATTA
* * * * * *
1204197 TGTAAGTTATTATGTAGGATATTATGTAAGTTATGTAAGTTTTTGTT-TT-
1 TGT--G-TATTATGTA--A-CTTATTTAATTTATGTAAGTATGTATTATTA
*
1204246 TGTGTATTATGTAACTTATTTAATTTATGTAGGGTATGTATTATTA
1 TGTGTATTATGTAACTTATTTAATTTATGTA-AGTATGTATTATTA
1204292 TGT
1 TGT
1204295 AAGTTATTAT
Statistics
Matches: 76, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
43 14 0.18
44 7 0.09
45 5 0.07
46 12 0.16
47 2 0.03
48 9 0.12
49 3 0.04
50 3 0.04
51 21 0.28
ACGTcount: A:0.28, C:0.01, G:0.17, T:0.53
Consensus pattern (45 bp):
TGTGTATTATGTAACTTATTTAATTTATGTAAGTATGTATTATTA
Found at i:1204315 original size:24 final size:24
Alignment explanation
Indices: 1204286--1204337 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
1204276 AGGGTATGTA
*
1204286 TTATTATGTAAGTTATTATGTAGG
1 TTATTATGTAAGTCATTATGTAGG
*
1204310 TTATTATGTAAGTCATTATGTTGG
1 TTATTATGTAAGTCATTATGTAGG
1204334 TTAT
1 TTAT
1204338 GTAAGTTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.27, C:0.02, G:0.19, T:0.52
Consensus pattern (24 bp):
TTATTATGTAAGTCATTATGTAGG
Found at i:1204339 original size:21 final size:22
Alignment explanation
Indices: 1204289--1204343 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 22
1204279 GTATGTATTA
*
1204289 TTATGTAAGTTATTATGTAGGTT
1 TTATGTAAGTCATTATGTAGG-T
*
1204312 ATTATGTAAGTCATTATGTTGG-
1 -TTATGTAAGTCATTATGTAGGT
1204334 TTATGTAAGT
1 TTATGTAAGT
1204344 TGTGATATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 10 0.34
24 19 0.66
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (22 bp):
TTATGTAAGTCATTATGTAGGT
Found at i:1204537 original size:9 final size:9
Alignment explanation
Indices: 1204523--1204603 Score: 60
Period size: 9 Copynumber: 9.0 Consensus size: 9
1204513 TAAATATTAA
1204523 TAAGTTATG
1 TAAGTTATG
1204532 TAAGTTATG
1 TAAGTTATG
* *
1204541 TATTA-TAAATT
1 TA--AGT-TATG
*
1204552 TAAATTATG
1 TAAGTTATG
1204561 TAAGTTATG
1 TAAGTTATG
1204570 -AA-TTATG
1 TAAGTTATG
1204577 TAAGTTATG
1 TAAGTTATG
* *
1204586 TAAATTACG
1 TAAGTTATG
*
1204595 TGAGTTATG
1 TAAGTTATG
1204604 AAATTTGAAC
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
7 5 0.09
8 4 0.07
9 40 0.71
10 2 0.04
11 5 0.09
ACGTcount: A:0.37, C:0.01, G:0.17, T:0.44
Consensus pattern (9 bp):
TAAGTTATG
Found at i:1204575 original size:16 final size:16
Alignment explanation
Indices: 1204527--1204605 Score: 74
Period size: 16 Copynumber: 5.0 Consensus size: 16
1204517 TATTAATAAG
*
1204527 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGAA
* *
1204543 TTA--TAAATT-TAAA
1 TTATGTAAGTTATGAA
1204556 TTATGTAAGTTATGAA
1 TTATGTAAGTTATGAA
1204572 TTATGTAAGTTATGTAAA
1 TTATGTAAGTTATG--AA
* *
1204590 TTACGTGAGTTATGAA
1 TTATGTAAGTTATGAA
1204606 ATTTGAACTT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
13 5 0.10
14 5 0.10
15 5 0.10
16 22 0.43
18 14 0.27
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.44
Consensus pattern (16 bp):
TTATGTAAGTTATGAA
Found at i:1204678 original size:34 final size:35
Alignment explanation
Indices: 1204620--1204699 Score: 135
Period size: 34 Copynumber: 2.3 Consensus size: 35
1204610 GAACTTTAAA
* *
1204620 AAAATTAAATATTTAAAAATATTCGTGATTAAAAT
1 AAAATAAAATATTTAAAAAAATTCGTGATTAAAAT
1204655 AAAATAAAATA-TTAAAAAAATTCGTGATTAAAAT
1 AAAATAAAATATTTAAAAAAATTCGTGATTAAAAT
1204689 AAAATAAAATA
1 AAAATAAAATA
1204700 AAATATTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
34 33 0.77
35 10 0.23
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (35 bp):
AAAATAAAATATTTAAAAAAATTCGTGATTAAAAT
Found at i:1206401 original size:44 final size:44
Alignment explanation
Indices: 1206338--1206424 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
1206328 TGGAAGGAGA
1206338 AAGGAGGCGATTTAGGGATTTGGGATTTCAAGAAATTCGGCAAG
1 AAGGAGGCGATTTAGGGATTTGGGATTTCAAGAAATTCGGCAAG
* *
1206382 AAGGAGGCGATTTATGGATTTGGGATTTCAAGAAATTGGGCAA
1 AAGGAGGCGATTTAGGGATTTGGGATTTCAAGAAATTCGGCAA
1206425 AAAGATTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.32, C:0.08, G:0.33, T:0.26
Consensus pattern (44 bp):
AAGGAGGCGATTTAGGGATTTGGGATTTCAAGAAATTCGGCAAG
Found at i:1207660 original size:15 final size:15
Alignment explanation
Indices: 1207628--1207667 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1207618 CCTAAACCCC
1207628 AAACCCTAAA-TCTT
1 AAACCCTAAACTCTT
*
1207642 AAACCCTAAACTTTT
1 AAACCCTAAACTCTT
1207657 AAACCCTAAAC
1 AAACCCTAAAC
1207668 CAAAAACACC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (15 bp):
AAACCCTAAACTCTT
Found at i:1208192 original size:115 final size:114
Alignment explanation
Indices: 1207983--1208615 Score: 572
Period size: 114 Copynumber: 5.5 Consensus size: 114
1207973 ATGCATGGTT
*
1207983 AAGACCAAAACTG-TGCGTTTTGGTTAAGATATTTTGCGGCGCTTCCCAAAAAGCGCCGCTAATA
1 AAGACCAAAAC-GCTGCGTTTTGGTTAAGATATTTTGCGGCGCTT-CTAAAAAGCGCCGCTAATA
* * * * * * *
1208047 ATATGCTTTAGCACCG-ATTTCTCGTGAGCGCCGCTAATTCCAGTATACATC
64 GTATGCTTTAGCAGCGTTTTTC-CATAAGCGCCACTAATTCTAGTATACATC
** * * * *
1208098 AAGACTTAAACGCAGCGTTTTAGTTAATATATTTTGCAGCGCTTCTAAAAACGCGCCGCTAATAG
1 AAGACCAAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTAAAAA-GCGCCGCTAATAG
* * *
1208163 TATGCTTTAGCAGCGTTTTTCCATAAGCGCCACTAATTCTAATACACCTC
65 TATGCTTTAGCAGCGTTTTTCCATAAGCGCCACTAATTCTAGTATACATC
* * * **
1208213 AAGACC-AAACTCTGCGTTTTGGTGT--GCATATCTTGCGGCGCTTATCGCAAAGCGCCGCTAAT
1 AAGACCAAAACGCTGCGTTTTGGT-TAAG-ATATTTTGCGGCGCTTCT-AAAAAGCGCCGCTAAT
* ** * *
1208275 ACTATTATTTAGC-G-GTGTTTTCTAGTAAGCGCCACTAATTATAGTATACATC
63 AGTATGCTTTAGCAGCGT-TTTTCCA-TAAGCGCCACTAATTCTAGTATACATC
* * * * * *
1208327 AAGACCAAAACGCTGAGTTTTGGTTAAGAAATTTAGCGGCGCTTCTCTAAACGCCCCGCTAATAG
1 AAGACCAAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCT-AAAAAGCGCCGCTAATAG
** * *** *
1208392 TACACTTTAGCGGCGTTTTT--AGTTTTCGCCACTAATTCTAGTATACTTC
65 TATGCTTTAGCAGCGTTTTTCCA-TAAGCGCCACTAATTCTAGTATACATC
* * *
1208441 AAGATC-AAA-GTCTGCTTTTTGGTTAAGATATTTTGCGGCGCTTCTAAAAAATCGCCGCTAAT-
1 AAGACCAAAACG-CTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCT-AAAAAGCGCCGCTAATA
* * * * *
1208503 GTTATGCTTTAGCGGCGTTTTTCCCTAA-CACCACTAATTGTATTATACATC
64 G-TATGCTTTAGCAGCGTTTTTCCATAAGCGCCACTAATTCTAGTATACATC
* * * * *
1208554 AAGACCAAAACGCTGCGTTTTGGTTAAGATTTTTTGCGGCACTTCTAATAAGCACCACTAAT
1 AAGACCAAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTAAAAAGCGCCGCTAAT
1208616 TCTACTATAC
Statistics
Matches: 418, Mismatches: 81, Indels: 40
0.78 0.15 0.07
Matches are distributed among these distances:
112 4 0.01
113 106 0.25
114 151 0.36
115 145 0.35
116 10 0.02
117 2 0.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (114 bp):
AAGACCAAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTAAAAAGCGCCGCTAATAGT
ATGCTTTAGCAGCGTTTTTCCATAAGCGCCACTAATTCTAGTATACATC
Found at i:1208402 original size:229 final size:227
Alignment explanation
Indices: 1207983--1208582 Score: 650
Period size: 229 Copynumber: 2.6 Consensus size: 227
1207973 ATGCATGGTT
* *
1207983 AAGACCAAAACTGTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCCCAAAAAGCGCCGCTAATAA
1 AAGACC-AAACTCTGCGTTTTGGTT-AGATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATAA
** * * * ** ** *
1208048 TATGCTTTAGCACCGATTTCTCGTGAGCGCCGCTAATTCCAGTATACATCAAGACTTAAACGCAG
64 TATGCTTTAGCGGCGTTTTCTCGTAAGCGCCACTAATTATAGTATACATCAAGACCAAAACGCTG
* * * * * **
1208113 CGTTTTAGTTAATATATTTTGCAGCGCTTCTAAAAACGCGCCGCTAATAGTATGCTTTAGCAGCG
129 CGTTTTGGTTAAGAAATTTAGCAGCGCTTCTAAAAACGCCCCGCTAATAGTACACTTTAGCAGCG
1208178 TTTTTCCA-TAAGCGCCACTAATTCTAATACACCTC
194 TTTTT--AGTAAGCGCCACTAATTCTAATACACCTC
* * ** *
1208213 AAGACCAAACTCTGCGTTTTGGTGT-GCATATCTTGCGGCGCTTATCGCAAAGCGCCGCTAATAC
1 AAGACCAAACTCTGCGTTTTGGT-TAG-ATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATAA
** * *
1208277 TATTATTTAGCGGTGTTTTCTAGTAAGCGCCACTAATTATAGTATACATCAAGACCAAAACGCTG
64 TATGCTTTAGCGGCGTTTTCTCGTAAGCGCCACTAATTATAGTATACATCAAGACCAAAACGCTG
* * ** *
1208342 AGTTTTGGTTAAGAAATTTAGCGGCGCTTCTCTAAACGCCCCGCTAATAGTACACTTTAGCGGCG
129 CGTTTTGGTTAAGAAATTTAGCAGCGCTTCTAAAAACGCCCCGCTAATAGTACACTTTAGCAGCG
*** * * *
1208407 TTTTTAGTTTTCGCCACTAATTCTAGTATACTTC
194 TTTTTAGTAAGCGCCACTAATTCTAATACACCTC
* * * * * **
1208441 AAGATCAAAGTCTGCTTTTTGGTTAAGATATTTTGCGGCGCTTCTAAAAAATCGCCGCTAATGTT
1 AAGACCAAACTCTGCGTTTTGGTT-AGATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATAAT
* * * *
1208506 ATGCTTTAGCGGCGTTTT-TCCCTAA-CACCACTAATTGTATTATACATCAAGACCAAAACGCTG
65 ATGCTTTAGCGGCGTTTTCT-CGTAAGCGCCACTAATTATAGTATACATCAAGACCAAAACGCTG
1208569 CGTTTTGGTTAAGA
129 CGTTTTGGTTAAGA
1208583 TTTTTTGCGG
Statistics
Matches: 305, Mismatches: 59, Indels: 15
0.80 0.16 0.04
Matches are distributed among these distances:
227 51 0.17
228 90 0.30
229 157 0.51
230 7 0.02
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (227 bp):
AAGACCAAACTCTGCGTTTTGGTTAGATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATAATA
TGCTTTAGCGGCGTTTTCTCGTAAGCGCCACTAATTATAGTATACATCAAGACCAAAACGCTGCG
TTTTGGTTAAGAAATTTAGCAGCGCTTCTAAAAACGCCCCGCTAATAGTACACTTTAGCAGCGTT
TTTAGTAAGCGCCACTAATTCTAATACACCTC
Found at i:1208681 original size:75 final size:75
Alignment explanation
Indices: 1208514--1208689 Score: 210
Period size: 75 Copynumber: 2.3 Consensus size: 75
1208504 TTATGCTTTA
* * * *
1208514 GCGGCGTTTTTCCCTAA-CACCACTAATTGTATTATACATCAAGACCAAAACGCTGCGTTTTGGT
1 GCGGCGCTTTT-CATAAGCACCACTAATTCTACTATACATCAAGACCAAAACGCTGCGTTTTGGT
* *
1208578 TAAGATTTTTT
65 TAACATATTTT
* * * * *
1208589 GCGGCACTTCTAATAAGCACCACTAATTCTACTATACATCAAGATCAAAACTCTGCGTTTTGGTT
1 GCGGCGCTTTTCATAAGCACCACTAATTCTACTATACATCAAGACCAAAACGCTGCGTTTTGGTT
*
1208654 ATCATATTTT
66 AACATATTTT
* *
1208664 GCGGCGCTTTTCGTAAGCGCCACTAA
1 GCGGCGCTTTTCATAAGCACCACTAA
1208690 GACTTGTTTT
Statistics
Matches: 83, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
74 3 0.04
75 80 0.96
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (75 bp):
GCGGCGCTTTTCATAAGCACCACTAATTCTACTATACATCAAGACCAAAACGCTGCGTTTTGGTT
AACATATTTT
Found at i:1208739 original size:187 final size:187
Alignment explanation
Indices: 1208420--1208784 Score: 416
Period size: 187 Copynumber: 2.0 Consensus size: 187
1208410 TTAGTTTTCG
* * * * *
1208420 CCACTAATTCTAGTATACTTCAAGATCAAAGTCTGCTTTTTGGTTAAGATATTTTGCGGCGCTTC
1 CCACTAATTCTACTATACATCAAGATCAAACTCTGCGTTTTGGTTAACATATTTTGCGGCGCTTC
* * * * *
1208485 TAAAAAATCGCCGCTAATGTTATGCTTTAGCGGCGTTTTTCCCTAACACCACTAATTGTATTATA
66 TAAAAAAGCGCCACTAATGCTATGCTTTAGCGGCGTTTTTCCCTAACACCACTAATTCTAATATA
* *
1208550 CATCAAG-ACCAAAACGCTGCGTTTTGGTTAAGATTTTTTGCGGCACTTCTAATAAGCA
131 CATC-AGTACCAAAACGATGCGTTTTGGTGAAG-TTTTTTGCGGCACTTCTAATAAGCA
*
1208608 CCACTAATTCTACTATACATCAAGATCAAAACTCTGCGTTTTGGTTATCATATTTTGCGGCGCTT
1 CCACTAATTCTACTATACATCAAGATC-AAACTCTGCGTTTTGGTTAACATATTTTGCGGCGCTT
**** * * ** *
1208673 -TTCGTAAGCGCCACTAA-GACT-TGTTTTAGTGGCGTTTTT-TGTAAGCGCCACTAATTCTAAT
65 CTAAAAAAGCGCCACTAATG-CTATGCTTTAGCGGCGTTTTTCCCTAA-CACCACTAATTCTAAT
* * * *
1208734 ATACATCGGTACCAAAACGATGCGTTTTTGTGGAGTTTTTTGCGGCGCTTC
128 ATACATCAGTACCAAAACGATGCGTTTTGGTGAAGTTTTTTGCGGCACTTC
1208785 CCACAATGCG
Statistics
Matches: 147, Mismatches: 26, Indels: 10
0.80 0.14 0.05
Matches are distributed among these distances:
186 19 0.13
187 58 0.39
188 37 0.25
189 33 0.22
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (187 bp):
CCACTAATTCTACTATACATCAAGATCAAACTCTGCGTTTTGGTTAACATATTTTGCGGCGCTTC
TAAAAAAGCGCCACTAATGCTATGCTTTAGCGGCGTTTTTCCCTAACACCACTAATTCTAATATA
CATCAGTACCAAAACGATGCGTTTTGGTGAAGTTTTTTGCGGCACTTCTAATAAGCA
Found at i:1209609 original size:15 final size:16
Alignment explanation
Indices: 1209585--1209617 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1209575 TTTTCAAAAT
*
1209585 AATATCATAAAAT-TA
1 AATATAATAAAATATA
1209600 AATATAATAAAATATA
1 AATATAATAAAATATA
1209616 AA
1 AA
1209618 GAAAGGGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AATATAATAAAATATA
Found at i:1209928 original size:41 final size:40
Alignment explanation
Indices: 1209817--1209928 Score: 95
Period size: 41 Copynumber: 2.8 Consensus size: 40
1209807 TCGGATAATT
* *
1209817 CGAAGCAATAAGTTGACACCCAGTGTCTCATCG-GCTAAAC
1 CGAAGTAATAA-TTGACACCCAGTGTCTCATCGAACTAAAC
** ** * * * *
1209857 CGAAGT-A-AATTGGTACCCAGTACCTTATCGAATTTATC
1 CGAAGTAATAATTGACACCCAGTGTCTCATCGAACTAAAC
1209895 CGAAGTAATAATTTGACACCCAGTGTCTCATCGA
1 CGAAGTAATAA-TTGACACCCAGTGTCTCATCGA
1209929 CACGAAGTCG
Statistics
Matches: 53, Mismatches: 15, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
37 16 0.30
38 11 0.21
39 2 0.04
40 7 0.13
41 17 0.32
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (40 bp):
CGAAGTAATAATTGACACCCAGTGTCTCATCGAACTAAAC
Found at i:1211604 original size:17 final size:17
Alignment explanation
Indices: 1211584--1211643 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
1211574 TTATTTATAA
1211584 AAAATTATAATTTTTTT
1 AAAATTATAATTTTTTT
* *
1211601 AAAAATATAATTTTTAT
1 AAAATTATAATTTTTTT
* *
1211618 AAATATTTTGAA-TTTTTG
1 AAA-ATTAT-AATTTTTTT
1211636 AAAATTAT
1 AAAATTAT
1211644 TTTGTTTTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
17 22 0.65
18 10 0.29
19 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
AAAATTATAATTTTTTT
Found at i:1211633 original size:19 final size:20
Alignment explanation
Indices: 1211609--1211647 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1211599 TTAAAAATAT
1211609 AATTTTT-ATAAA-TATTTTG
1 AATTTTTGA-AAATTATTTTG
1211628 AATTTTTGAAAATTATTTTG
1 AATTTTTGAAAATTATTTTG
1211648 TTTTTGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (20 bp):
AATTTTTGAAAATTATTTTG
Found at i:1211824 original size:32 final size:32
Alignment explanation
Indices: 1211787--1211849 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
1211777 TTGAACTCGG
* *
1211787 AACTCAAATTA-TTTATTCGAGTTAACTCGAAT
1 AACTCAAATAACTTGATTCGA-TTAACTCGAAT
*
1211819 AACTCAAATAACTTGATTCGATTACCTCGAA
1 AACTCAAATAACTTGATTCGATTAACTCGAA
1211850 ATTCAAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 19 0.70
33 8 0.30
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (32 bp):
AACTCAAATAACTTGATTCGATTAACTCGAAT
Found at i:1213801 original size:30 final size:29
Alignment explanation
Indices: 1213730--1213815 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
1213720 TTTAGTGCTT
* * *
1213730 AAAAAGTATGTGTTATATTTTTATAATAA
1 AAAAAATATGTATTACATTTTTATAATAA
*
1213759 AAAAATTATGTATTACATTTTTATAATAA
1 AAAAAATATGTATTACATTTTTATAATAA
* *
1213788 AAAATAATGTGTATTGCATTTTTATAAT
1 AAAA-AATATGTATTACATTTTTATAAT
1213816 TAAATATATG
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
29 30 0.60
30 20 0.40
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.45
Consensus pattern (29 bp):
AAAAAATATGTATTACATTTTTATAATAA
Found at i:1213827 original size:27 final size:28
Alignment explanation
Indices: 1213736--1213829 Score: 100
Period size: 30 Copynumber: 3.3 Consensus size: 28
1213726 GCTTAAAAAG
* * *
1213736 TATGTGTTATATTTTTATAATAAAAAAA
1 TATGTATTACATTTTTATAATAAAAATA
1213764 TTATGTATTACATTTTTATAATAAAAAATAA
1 -TATGTATTACATTTTTATAAT-AAAAAT-A
* * *
1213795 TGTGTATTGCATTTTTATAAT-TAAATA
1 TATGTATTACATTTTTATAATAAAAATA
1213822 TATGTATT
1 TATGTATT
1213830 TAAAAAATGT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
27 8 0.14
28 4 0.07
29 19 0.34
30 24 0.43
31 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (28 bp):
TATGTATTACATTTTTATAATAAAAATA
Found at i:1216436 original size:15 final size:16
Alignment explanation
Indices: 1216407--1216436 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1216397 ACTTCCGCAT
1216407 TTTTTTAAATGATTTG
1 TTTTTTAAATGATTTG
1216423 TTTTTTAAAT-ATTT
1 TTTTTTAAATGATTT
1216437 AAATTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (16 bp):
TTTTTTAAATGATTTG
Found at i:1216482 original size:27 final size:27
Alignment explanation
Indices: 1216452--1216507 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
1216442 TATTTAGTGC
* *
1216452 TTAAAAATATGTGTTATATTTTTATAA
1 TTAAAAATACGTGTTACATTTTTATAA
* * *
1216479 TTAAAAGTGCGTGTTGCATTTTTATAA
1 TTAAAAATACGTGTTACATTTTTATAA
1216506 TT
1 TT
1216508 GAATATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.12, T:0.50
Consensus pattern (27 bp):
TTAAAAATACGTGTTACATTTTTATAA
Found at i:1218615 original size:30 final size:32
Alignment explanation
Indices: 1218554--1218618 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
1218544 TAACACTAAT
* * **
1218554 AATAATAATAATAATGTTAAAATAATTAACTA
1 AATAATAATAATAATGCTAAAAAAACAAACTA
1218586 AATAATAA-AA-AATGCTAAAAAAACAAACTA
1 AATAATAATAATAATGCTAAAAAAACAAACTA
1218616 AAT
1 AAT
1218619 CGAAATGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 19 0.66
31 2 0.07
32 8 0.28
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (32 bp):
AATAATAATAATAATGCTAAAAAAACAAACTA
Found at i:1219568 original size:23 final size:22
Alignment explanation
Indices: 1219541--1219584 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1219531 TAGGGTTATT
1219541 TTGGGCCTGGGGTATTGGGTTTG
1 TTGGG-CTGGGGTATTGGGTTTG
* *
1219564 TTGGGTTTGGGTATTGGGTTT
1 TTGGGCTGGGGTATTGGGTTT
1219585 AATTTTGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.05, C:0.05, G:0.45, T:0.45
Consensus pattern (22 bp):
TTGGGCTGGGGTATTGGGTTTG
Found at i:1220069 original size:20 final size:20
Alignment explanation
Indices: 1220044--1220083 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1220034 GGTAGGCAGT
*
1220044 GACGTGACCATGGCGGTGGC
1 GACGTGACCATGGCAGTGGC
*
1220064 GACGTGACCGTGGCAGTGGC
1 GACGTGACCATGGCAGTGGC
1220084 AGGGCTAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.25, G:0.45, T:0.15
Consensus pattern (20 bp):
GACGTGACCATGGCAGTGGC
Found at i:1220216 original size:23 final size:22
Alignment explanation
Indices: 1220189--1220232 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1220179 TAGGGTTATT
1220189 TTGGGCCTGGGGTATTGGGTTTG
1 TTGGG-CTGGGGTATTGGGTTTG
* *
1220212 TTGGGTTTGGGTATTGGGTTT
1 TTGGGCTGGGGTATTGGGTTT
1220233 AATTTTGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.05, C:0.05, G:0.45, T:0.45
Consensus pattern (22 bp):
TTGGGCTGGGGTATTGGGTTTG
Found at i:1220709 original size:27 final size:27
Alignment explanation
Indices: 1220640--1220709 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
1220630 TATTTAATGC
* *
1220640 TTAAAAATGATGTATTAAATTTTTATAA
1 TTAAAAAT-ATGTATTAAATTGTTACAA
** **
1220668 TTAAAAATACATATTGCATTGTTACAA
1 TTAAAAATATGTATTAAATTGTTACAA
1220695 TTAAAAATATGTATT
1 TTAAAAATATGTATT
1220710 TCAAAAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
27 26 0.76
28 8 0.24
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (27 bp):
TTAAAAATATGTATTAAATTGTTACAA
Found at i:1221890 original size:4 final size:4
Alignment explanation
Indices: 1221881--1221906 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1221871 TAAACTAACC
1221881 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
1221907 ATTAACCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1224351 original size:13 final size:15
Alignment explanation
Indices: 1224322--1224353 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
1224312 AGAAGGGGGA
1224322 AATTTTATTTAATTT
1 AATTTTATTTAATTT
1224337 AATTTT-TTT-ATTT
1 AATTTTATTTAATTT
1224350 AATT
1 AATT
1224354 AAAAATGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 3 0.18
15 6 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
AATTTTATTTAATTT
Found at i:1227713 original size:19 final size:18
Alignment explanation
Indices: 1227689--1227724 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1227679 TAGTTAATTA
*
1227689 TTTAATAGTACAATTTTAT
1 TTTAATAATA-AATTTTAT
1227708 TTTAATAATAAATTTTA
1 TTTAATAATAAATTTTA
1227725 ACAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTAATAATAAATTTTAT
Found at i:1227818 original size:25 final size:27
Alignment explanation
Indices: 1227772--1227827 Score: 80
Period size: 25 Copynumber: 2.1 Consensus size: 27
1227762 ATATTATTGG
*
1227772 AAATATTTATATTAATATTTTAATAAT
1 AAATATATATATTAATATTTTAATAAT
*
1227799 AAATATATATA-TCATA-TTTAATAAT
1 AAATATATATATTAATATTTTAATAAT
1227824 AAAT
1 AAAT
1227828 GTTTTATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 13 0.48
26 4 0.15
27 10 0.37
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (27 bp):
AAATATATATATTAATATTTTAATAAT
Found at i:1229644 original size:42 final size:43
Alignment explanation
Indices: 1229595--1229813 Score: 187
Period size: 43 Copynumber: 5.1 Consensus size: 43
1229585 CGTTTATGTG
*
1229595 AAAAACGCCACTATAG-ACATGACCTTTAGCAACG-TTTCTCAC
1 AAAAACGCCACTAAAGAACATGACCTTTAGCAACGCTTT-TCAC
* * * * *
1229637 AAAAACGCCACTATAGAACATAACCTCTAGCAGCGCTTTTAAC
1 AAAAACGCCACTAAAGAACATGACCTTTAGCAACGCTTTTCAC
* * *
1229680 ACAAATG-TAGCTAAAGAACATGACCTTTAGCAACGCTTTTC-C
1 AAAAACGCCA-CTAAAGAACATGACCTTTAGCAACGCTTTTCAC
* * ****
1229722 AATAAATGCCACTAAAGAACATGACATTTAATGGCGC-TTTCAC
1 AA-AAACGCCACTAAAGAACATGACCTTTAGCAACGCTTTTCAC
* * * ** *
1229765 ACAAACGCCGCTAAAAAACATGACCTTTAGCGGCGCTTTTCCC
1 AAAAACGCCACTAAAGAACATGACCTTTAGCAACGCTTTTCAC
1229808 AAAAAC
1 AAAAAC
1229814 ATAAGCTAAG
Statistics
Matches: 142, Mismatches: 28, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
42 51 0.36
43 87 0.61
44 4 0.03
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.23
Consensus pattern (43 bp):
AAAAACGCCACTAAAGAACATGACCTTTAGCAACGCTTTTCAC
Found at i:1229759 original size:86 final size:84
Alignment explanation
Indices: 1229611--1229813 Score: 219
Period size: 86 Copynumber: 2.4 Consensus size: 84
1229601 GCCACTATAG
* * *
1229611 ACATGACCTTTAGCAACG-TTTCTCACAAAAACGCCACTATAGAACATAACCTCTAGCAGCGCTT
1 ACATGACCTTTAGCAACGCTTT-TC-CAAAAACGCCACTAAAGAACATAACATCTAACAGCGC-T
* * *
1229675 TTAACACAAATGTAGCTAAAGA
63 TTAACACAAACGCAGCTAAAAA
* * * **
1229697 ACATGACCTTTAGCAACGCTTTTCCAATAAATGCCACTAAAGAACATGACATTTAATGGCGCTTT
1 ACATGACCTTTAGCAACGCTTTTCCAA-AAACGCCACTAAAGAACATAACATCTAACAGCGCTTT
* *
1229762 CACACAAACGCCGCTAAAAA
65 AACACAAACGCAGCTAAAAA
**
1229782 ACATGACCTTTAGCGGCGCTTTTCCCAAAAAC
1 ACATGACCTTTAGCAACGCTTTT-CCAAAAAC
1229814 ATAAGCTAAG
Statistics
Matches: 98, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
85 45 0.46
86 50 0.51
87 3 0.03
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (84 bp):
ACATGACCTTTAGCAACGCTTTTCCAAAAACGCCACTAAAGAACATAACATCTAACAGCGCTTTA
ACACAAACGCAGCTAAAAA
Found at i:1230948 original size:25 final size:23
Alignment explanation
Indices: 1230895--1230952 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
1230885 CGCCAATGCG
* * *
1230895 GCAGAGGAGTGTAACGGCGATGC
1 GCAGAGGAGGGTAACGACGATAC
1230918 GACAGAGGAGGGTCAACGACGATAC
1 G-CAGAGGAGGGT-AACGACGATAC
1230943 AGCAGAGGAG
1 -GCAGAGGAG
1230953 ACAGTCGACG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 1 0.03
24 10 0.34
25 17 0.59
26 1 0.03
ACGTcount: A:0.33, C:0.17, G:0.41, T:0.09
Consensus pattern (23 bp):
GCAGAGGAGGGTAACGACGATAC
Found at i:1231734 original size:22 final size:22
Alignment explanation
Indices: 1231678--1231739 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
1231668 TATACGGAAA
* *
1231678 TAAATCCTAAACCCTAAAACTC
1 TAAACCCTAAACCTTAAAACTC
* *
1231700 TAAACCTTCAACCTTAAAACTC
1 TAAACCCTAAACCTTAAAACTC
1231722 TAAACCCTAAACCTTAAA
1 TAAACCCTAAACCTTAAA
1231740 CATTGAACCT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAACCCTAAACCTTAAAACTC
Found at i:1231783 original size:14 final size:15
Alignment explanation
Indices: 1231753--1231797 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
1231743 TGAACCTTAA
1231753 AAATCATAAA-TCCT
1 AAATCATAAACTCCT
*
1231767 AAATCATAAACT-TT
1 AAATCATAAACTCCT
*
1231781 AAATCTTAAAC-CCT
1 AAATCATAAACTCCT
1231795 AAA
1 AAA
1231798 ATAAAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 25 0.96
15 1 0.04
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATCATAAACTCCT
Found at i:1231789 original size:37 final size:36
Alignment explanation
Indices: 1231679--1231790 Score: 100
Period size: 37 Copynumber: 3.0 Consensus size: 36
1231669 ATACGGAAAT
* *
1231679 AAATCCTAAACCCTAAAACTC-TAAACCTTCAACCTTAA
1 AAAT-CTAAACCCT-AAAC-CATAAACATTAAACCTTAA
* * *
1231717 AACTCTAAACCCTAAACCTTAAACATTGAACCTTAA
1 AAATCTAAACCCTAAACCATAAACATTAAACCTTAA
* * * *
1231753 AAATCATAAATCCTAAATCATAAACTTTAAATCTTAA
1 AAATC-TAAACCCTAAACCATAAACATTAAACCTTAA
1231790 A
1 A
1231791 CCCTAAAATA
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
35 1 0.02
36 23 0.37
37 35 0.56
38 3 0.05
ACGTcount: A:0.47, C:0.25, G:0.01, T:0.27
Consensus pattern (36 bp):
AAATCTAAACCCTAAACCATAAACATTAAACCTTAA
Found at i:1232166 original size:84 final size:84
Alignment explanation
Indices: 1232040--1232215 Score: 298
Period size: 84 Copynumber: 2.1 Consensus size: 84
1232030 CAAGCCAAAT
1232040 GCCACTAAAAAACTTAATTCCCTATAGTGAAACGACGACGTTTAAGTCAAATTGGCATTGCAATT
1 GCCACT-AAAAACTTAATTCCCTATAGTGAAACGACGACGTTTAAGTCAAATTGGCATTGCAATT
1232105 TTGCGGCGTTTATGAAAAAC
65 TTGCGGCGTTTATGAAAAAC
* * * *
1232125 GCCACTAAAAACTTAATTCCCTATAGTGAAACGACGCCGTTTAAGTCAAATTGGTATTGTATTTT
1 GCCACTAAAAACTTAATTCCCTATAGTGAAACGACGACGTTTAAGTCAAATTGGCATTGCAATTT
*
1232190 TGCGGCGTTTATGAAAAAT
66 TGCGGCGTTTATGAAAAAC
1232209 GCCACTA
1 GCCACTA
1232216 TTGTATAACC
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
84 80 0.93
85 6 0.07
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (84 bp):
GCCACTAAAAACTTAATTCCCTATAGTGAAACGACGACGTTTAAGTCAAATTGGCATTGCAATTT
TGCGGCGTTTATGAAAAAC
Found at i:1232255 original size:209 final size:207
Alignment explanation
Indices: 1231948--1232339 Score: 572
Period size: 209 Copynumber: 1.9 Consensus size: 207
1231938 CTAACAAAAT
*
1231948 GACGTCGTTTAAATCAAATTGGTATTGCAATTTTGCGGCGTTTATGAAAAACGCCACTAATATAT
1 GACGCCGTTTAAATCAAATTGGTATTGCAATTTTGCGGCGTTTATGAAAAACGCCACTAATATAT
* * *
1232013 AACCTTTGCGACGTTTTCAAGCCAAATGCCACTAAAAAACTTAATTCCCTATAGTGAAACGACGA
66 AACCTTTGCGACGTTTTCAAGCAAAACGCCACT-AAAAACTTAATTCCCTATAGTGAAACAAC-A
*
1232078 -CGTTTAAGTCAAATTGGCATTGCAATTTTGCGGCGTTTATGAAAAACGCCACTAAAAACTTAAT
129 CCGTTTAAGTCAAATTGGAATTGCAATTTTGCGGCGTTTATG-AAAACGCCACTAAAAACTTAAT
1232142 TCCCTATAGTGAAAC
193 TCCCTATAGTGAAAC
* * * * * *
1232157 GACGCCGTTTAAGTCAAATTGGTATTGTATTTTTGCGGCGTTTATGAAAAATGCCACTATTGTAT
1 GACGCCGTTTAAATCAAATTGGTATTGCAATTTTGCGGCGTTTATGAAAAACGCCACTAATATAT
* * * *
1232222 AACCTTTGCGGCGTTTTC-GGTCAAAACGCCACTAAAACCTTAATTCCCTGTAGTGAAACAACAC
66 AACCTTTGCGACGTTTTCAAG-CAAAACGCCACTAAAAACTTAATTCCCTATAGTGAAACAACAC
* * *
1232286 CGTTTAAGTCAAATTTGAATTGTAATTTTGCGGCGTTTATGAAAATGCCACTAA
130 CGTTTAAGTCAAATTGGAATTGCAATTTTGCGGCGTTTATGAAAACGCCACTAA
1232340 TGTATAACCT
Statistics
Matches: 163, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
207 13 0.08
208 65 0.40
209 85 0.52
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (207 bp):
GACGCCGTTTAAATCAAATTGGTATTGCAATTTTGCGGCGTTTATGAAAAACGCCACTAATATAT
AACCTTTGCGACGTTTTCAAGCAAAACGCCACTAAAAACTTAATTCCCTATAGTGAAACAACACC
GTTTAAGTCAAATTGGAATTGCAATTTTGCGGCGTTTATGAAAACGCCACTAAAAACTTAATTCC
CTATAGTGAAAC
Found at i:1232376 original size:123 final size:122
Alignment explanation
Indices: 1232120--1232528 Score: 514
Period size: 124 Copynumber: 3.3 Consensus size: 122
1232110 GCGTTTATGA
* * *
1232120 AAAACGCCACTAAAAACTTAATTCCCTATAGTGAAACGACGCCGTTTAAGTCAAATTGGTATTGT
1 AAAACGCCACTAAAAACTTAATT-CCTGTAGTGAAACAACACCGTTTAAGTCAAATTGGTATTGT
* * *
1232185 ATTTTTGCGGCGTTTATGAAAAATGCCACTATTGTATAACCTTTGCGGCGTTTTCGGTC
65 AATTTTGCGGCGTTTATG-AAAATGCCACTAATGTATAACCTTTGCGGCGTTTTCAGTC
* * *
1232244 AAAACGCCACTAAAACCTTAATTCCCTGTAGTGAAACAACACCGTTTAAGTCAAATTTGAATTGT
1 AAAACGCCACTAAAAACTTAATT-CCTGTAGTGAAACAACACCGTTTAAGTCAAATTGGTATTGT
*
1232309 AATTTTGCGGCGTTTATGAAAATGCCACTAATGTATAACCTTTGCAGCGTTTTCAGTC
65 AATTTTGCGGCGTTTATGAAAATGCCACTAATGTATAACCTTTGCGGCGTTTTCAGTC
* * * * * *
1232367 AAAATGCCACTAAAAATTTAATGTTCTGTAGTGAAACAACGA-TGTTTAACTCGAATTGGTATTG
1 AAAACGCCACTAAAAACTTAAT-TCCTGTAGTGAAACAAC-ACCGTTTAAGTCAAATTGGTATTG
* * * * * * *
1232431 CAATTTTGCGGCGTTTATAAAAAACGCCACTAATGTATCACCTTTACGGCATTTTCAATC
64 TAATTTTGCGGCGTTTAT-GAAAATGCCACTAATGTATAACCTTTGCGGCGTTTTCAGTC
* *
1232491 AAAACGCTACTAAAAAAACTTACTTCCTGTAGTGAAAC
1 AAAACGCCACT--AAAAACTTAATTCCTGTAGTGAAAC
1232529 GGCATCGTTT
Statistics
Matches: 248, Mismatches: 32, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
123 105 0.42
124 121 0.49
125 13 0.05
126 9 0.04
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (122 bp):
AAAACGCCACTAAAAACTTAATTCCTGTAGTGAAACAACACCGTTTAAGTCAAATTGGTATTGTA
ATTTTGCGGCGTTTATGAAAATGCCACTAATGTATAACCTTTGCGGCGTTTTCAGTC
Found at i:1237476 original size:41 final size:41
Alignment explanation
Indices: 1237409--1237489 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 41
1237399 GCGGTAGGCA
1237409 TTTTTTCTTTTGTAATTTTCATTTTATTTTCGGCTATATANG
1 TTTTTTCTTTTGTAATTTTCATTTTATTTTCGGCTATATA-G
1237451 TTTTTTCTTTTGTAATTTTCA-TTTATTTTCGGCTATATA
1 TTTTTTCTTTTGTAATTTTCATTTTATTTTCGGCTATATA
1237490 AAGCCATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
41 18 0.46
42 21 0.54
ACGTcount: A:0.17, C:0.10, G:0.09, T:0.63
Consensus pattern (41 bp):
TTTTTTCTTTTGTAATTTTCATTTTATTTTCGGCTATATAG
Found at i:1254812 original size:24 final size:25
Alignment explanation
Indices: 1254766--1254814 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1254756 CCAATAATGG
*
1254766 TTATAATTTTTCAATTTTCAATTTT
1 TTATAATTTTTCAATGTTCAATTTT
1254791 TTATAATTTTT-AATGGTT-AATTTT
1 TTATAATTTTTCAAT-GTTCAATTTT
1254815 ATTTTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (25 bp):
TTATAATTTTTCAATGTTCAATTTT
Found at i:1255072 original size:15 final size:15
Alignment explanation
Indices: 1255052--1255081 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1255042 TATTTTATTA
1255052 ATATTTAAAAATCAT
1 ATATTTAAAAATCAT
*
1255067 ATATTTTAAAATCAT
1 ATATTTAAAAATCAT
1255082 GATGTAAGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATTTAAAAATCAT
Found at i:1260467 original size:20 final size:20
Alignment explanation
Indices: 1260444--1260489 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1260434 TGTTAATATT
1260444 TTGTTA-TTAATTCAAATAGG
1 TTGTTACTT-ATTCAAATAGG
* *
1260464 TTGTTACTTGTTTAAATAGG
1 TTGTTACTTATTCAAATAGG
1260484 TTGTTA
1 TTGTTA
1260490 AGATTTACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.50
Consensus pattern (20 bp):
TTGTTACTTATTCAAATAGG
Found at i:1264516 original size:46 final size:46
Alignment explanation
Indices: 1264449--1264587 Score: 224
Period size: 46 Copynumber: 3.0 Consensus size: 46
1264439 ACATTGCTAT
* * **
1264449 AACTCAGTATGGCTTTCTTCACGGAATTACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
* *
1264495 AACTCGGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1264541 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1264587 A
1 A
1264588 CTTTGCCATG
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 86 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.34
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
Found at i:1267992 original size:20 final size:20
Alignment explanation
Indices: 1267969--1268014 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1267959 TGTTAATATT
1267969 TTGTTA-TTAATTCAAATAGG
1 TTGTTACTT-ATTCAAATAGG
* *
1267989 TTGTTACTTGTTTAAATAGG
1 TTGTTACTTATTCAAATAGG
1268009 TTGTTA
1 TTGTTA
1268015 AGATTTACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.50
Consensus pattern (20 bp):
TTGTTACTTATTCAAATAGG
Found at i:1272886 original size:10 final size:10
Alignment explanation
Indices: 1272871--1272909 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
1272861 GGAGGATGTC
1272871 TATATTAAAT
1 TATATTAAAT
1272881 TATATTAAA-
1 TATATTAAAT
*
1272890 TATATATAGAT
1 TATAT-TAAAT
1272901 TATATTAAA
1 TATATTAAA
1272910 AATGGACAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 5 0.20
10 15 0.60
11 5 0.20
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (10 bp):
TATATTAAAT
Found at i:1278442 original size:3 final size:3
Alignment explanation
Indices: 1278434--1278461 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1278424 ATTTAAGACA
1278434 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1278462 TAGAAGCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1282423 original size:21 final size:23
Alignment explanation
Indices: 1282385--1282429 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1282375 TTTAAAAGTA
*
1282385 AAATATATATAATTTATT-TTTTT
1 AAATATAAATAA-TTATTATTTTT
1282408 AAATATAAATAA-TATTATTTTT
1 AAATATAAATAATTATTATTTTT
1282430 TGTGAATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 5 0.25
23 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AAATATAAATAATTATTATTTTT
Found at i:1282437 original size:25 final size:24
Alignment explanation
Indices: 1282385--1282447 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 24
1282375 TTTAAAAGTA
*
1282385 AAATATATATAAT-TTATTTTTTT
1 AAATATAAATAATATTATTTTTTT
1282408 AAATATAAATAATATTATTTTTTGT
1 AAATATAAATAATATTATTTTTT-T
* *
1282433 GAATACAAATAATAT
1 AAATATAAATAATAT
1282448 AAATTTAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 12 0.34
24 9 0.26
25 14 0.40
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (24 bp):
AAATATAAATAATATTATTTTTTT
Found at i:1284468 original size:15 final size:15
Alignment explanation
Indices: 1284448--1284479 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1284438 TTCTAATTTT
*
1284448 TAAATAGAAAGATAA
1 TAAATAAAAAGATAA
1284463 TAAATAAAAAGATAA
1 TAAATAAAAAGATAA
1284478 TA
1 TA
1284480 CGTTTTAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (15 bp):
TAAATAAAAAGATAA
Found at i:1288298 original size:16 final size:16
Alignment explanation
Indices: 1288277--1288339 Score: 58
Period size: 15 Copynumber: 4.0 Consensus size: 16
1288267 AAATTATGTC
*
1288277 AACAAATAATTATTTT
1 AACAAATAATTATATT
**
1288293 GGCAAA-AATTATATT
1 AACAAATAATTATATT
*
1288308 AACAAATAATTA-CTT
1 AACAAATAATTATATT
*
1288323 AACTAACTAATTATATT
1 AAC-AAATAATTATATT
1288340 TCTAATGTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
15 17 0.47
16 17 0.47
17 2 0.06
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (16 bp):
AACAAATAATTATATT
Found at i:1297018 original size:55 final size:56
Alignment explanation
Indices: 1296930--1297044 Score: 169
Period size: 55 Copynumber: 2.0 Consensus size: 56
1296920 AACCTCCCCC
* *
1296930 GCCCCCCCCCAAAAAAAAAAAAGAACGAAAGAAAGAAAAAGAAGCATCGATTCCAAAT
1 GCCCCCCCCCAAAAAAAAAAAAG-A-GAAAGAAAGAAAAAGAAGAATCAATTCCAAAT
**
1296988 GCCCCCCCCCCCAAAAAAAAAAG-GAAAGAAAGAAAAAGAAGAATCAATTCCAAAT
1 GCCCCCCCCCAAAAAAAAAAAAGAGAAAGAAAGAAAAAGAAGAATCAATTCCAAAT
1297043 GC
1 GC
1297045 TAAATTCTCA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
55 32 0.60
58 21 0.40
ACGTcount: A:0.54, C:0.25, G:0.14, T:0.07
Consensus pattern (56 bp):
GCCCCCCCCCAAAAAAAAAAAAGAGAAAGAAAGAAAAAGAAGAATCAATTCCAAAT
Found at i:1300521 original size:23 final size:23
Alignment explanation
Indices: 1300494--1300569 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
1300484 AGTGTTATTG
*
1300494 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
1300517 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
1300540 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1300563 ATCAGTG
1 ATCAGTG
1300570 TTGCACTTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:1304051 original size:25 final size:25
Alignment explanation
Indices: 1304023--1304150 Score: 79
Period size: 25 Copynumber: 5.2 Consensus size: 25
1304013 AATAACGGGT
*
1304023 AGCTTCAAAGAGCCATTAATCGGGA
1 AGCTTCAAAGAGCCATTAATCAGGA
* * **
1304048 AGC-TCTAAATAGCTA-TATATTGGGA
1 AGCTTC-AAAGAGCCATTA-ATCAGGA
*
1304073 AG-TTCAAGCGAGCCA-T-ATCAGGA
1 AGCTTCAA-AGAGCCATTAATCAGGA
**
1304096 AGC-TCTGGAGAGCCATTAATCAGGA
1 AGCTTC-AAAGAGCCATTAATCAGGA
* *
1304121 AGCTCACAAAGAGCCTTTAATCAGGA
1 AGCT-TCAAAGAGCCATTAATCAGGA
1304147 AGCT
1 AGCT
1304151 CACGAAAAGT
Statistics
Matches: 78, Mismatches: 15, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
23 15 0.19
24 7 0.09
25 35 0.45
26 20 0.26
27 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (25 bp):
AGCTTCAAAGAGCCATTAATCAGGA
Found at i:1304140 original size:26 final size:26
Alignment explanation
Indices: 1304104--1304153 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
1304094 GAAGCTCTGG
1304104 AGAGCCATTAATCAGGAAGCTCACAA
1 AGAGCCATTAATCAGGAAGCTCACAA
*
1304130 AGAGCCTTTAATCAGGAAGCTCAC
1 AGAGCCATTAATCAGGAAGCTCAC
1304154 GAAAAGTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (26 bp):
AGAGCCATTAATCAGGAAGCTCACAA
Found at i:1306079 original size:18 final size:18
Alignment explanation
Indices: 1306056--1306093 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1306046 ACTGACTTGT
*
1306056 ACCACACGGCCAAGCCAC
1 ACCACAAGGCCAAGCCAC
1306074 ACCACAAGGCCAAGCCAC
1 ACCACAAGGCCAAGCCAC
1306092 AC
1 AC
1306094 GCCCGTGTGC
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:0.37, C:0.47, G:0.16, T:0.00
Consensus pattern (18 bp):
ACCACAAGGCCAAGCCAC
Found at i:1308989 original size:11 final size:11
Alignment explanation
Indices: 1308969--1309007 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
1308959 TTTAACCTTC
1308969 AATATATTTTT
1 AATATATTTTT
1308980 AATA-ATTTTT
1 AATATATTTTT
1308990 AATATATTTTT
1 AATATATTTTT
*
1309001 AAAATAT
1 AATATAT
1309008 GTTGACCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AATATATTTTT
Found at i:1311692 original size:42 final size:42
Alignment explanation
Indices: 1311545--1311780 Score: 267
Period size: 42 Copynumber: 5.6 Consensus size: 42
1311535 ATGTCGTTAT
* * * * *
1311545 AGAACATGGCCTTTAACGGTGCTTTCCCCACAAATGCCACTAA
1 AGAACATGACCTTTAGCGGCGCTTT-CCCACAAACGCCGCTAA
* * *
1311588 AGAACATGACCTTCAGCGGCGCTTTCCCACAAACGCTG-TTA
1 AGAACATGACCTTTAGCGGCGCTTTCCCACAAACGCCGCTAA
* *
1311629 AGAACATGACTTTTAGTGGCGCTTTCCCACAAACGCCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTTCCCACAAACGCCGCTAA
* * * * *
1311671 AGAACATGACTTTTAGCGGCGCTTTTCCAAAAACACCACTAA
1 AGAACATGACCTTTAGCGGCGCTTTCCCACAAACGCCGCTAA
* * *
1311713 AGAATATGACCTTTAGCGGCGCTTTCCTCACAAATGCCGCCAA
1 AGAACATGACCTTTAGCGGCGCTTTCC-CACAAACGCCGCTAA
* *
1311756 AAAACATGACCTTTAGCGACGCTTT
1 AGAACATGACCTTTAGCGGCGCTTT
1311781 TCCCTAAAAC
Statistics
Matches: 162, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
41 36 0.22
42 73 0.45
43 53 0.33
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (42 bp):
AGAACATGACCTTTAGCGGCGCTTTCCCACAAACGCCGCTAA
Found at i:1312247 original size:66 final size:66
Alignment explanation
Indices: 1312164--1312291 Score: 186
Period size: 66 Copynumber: 1.9 Consensus size: 66
1312154 AAGCTGTAGC
* * * *
1312164 TGGAGTTCGTCATATTTTCTATT-TGCCTCTGCTTCCCTCGCTGCTGCCTCCGCTTTAAGTTGTA
1 TGGAGTTCGTCATATTTTCT-TTGAGCCTCTACTTCCCTCGATACTGCCTCCGCTTTAAGTTGTA
1312228 CT
65 CT
* *
1312230 TGGAGTTCTTCATATTTTCTTTGAGCCTCTACTTCTCTCGATACTGCCTCCGCTTTAAGTTG
1 TGGAGTTCGTCATATTTTCTTTGAGCCTCTACTTCCCTCGATACTGCCTCCGCTTTAAGTTG
1312292 AGCAATTTGC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 2 0.04
66 53 0.96
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.43
Consensus pattern (66 bp):
TGGAGTTCGTCATATTTTCTTTGAGCCTCTACTTCCCTCGATACTGCCTCCGCTTTAAGTTGTAC
T
Found at i:1314008 original size:20 final size:20
Alignment explanation
Indices: 1313983--1314023 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1313973 ATCTTCATCC
1313983 ACATCTTGGCGAACCCATTG
1 ACATCTTGGCGAACCCATTG
1314003 ACATCTTGGCGAACCCATTG
1 ACATCTTGGCGAACCCATTG
1314023 A
1 A
1314024 AATTGTGTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (20 bp):
ACATCTTGGCGAACCCATTG
Found at i:1317504 original size:13 final size:13
Alignment explanation
Indices: 1317486--1317510 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1317476 CACGAATATG
1317486 CCAATTGATGTTA
1 CCAATTGATGTTA
1317499 CCAATTGATGTT
1 CCAATTGATGTT
1317511 GCCACACTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
CCAATTGATGTTA
Found at i:1318337 original size:19 final size:18
Alignment explanation
Indices: 1318315--1318353 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1318305 ATTTAGAATC
*
1318315 AAAACTAAATTAAATAATA
1 AAAAATAAATTAAAT-ATA
*
1318334 AAAAATGAATTAAATATA
1 AAAAATAAATTAAATATA
1318352 AA
1 AA
1318354 GATATCAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATAAATTAAATATA
Found at i:1320360 original size:10 final size:10
Alignment explanation
Indices: 1320345--1320399 Score: 65
Period size: 10 Copynumber: 5.3 Consensus size: 10
1320335 AACTGAAACA
1320345 TCATTTTGAG
1 TCATTTTGAG
*
1320355 TCATTTTCGAA
1 TCATTTT-GAG
1320366 TCATTTTGAG
1 TCATTTTGAG
* *
1320376 TCACTTTCGAA
1 TCA-TTTTGAG
1320387 TCATTTTGAG
1 TCATTTTGAG
1320397 TCA
1 TCA
1320400 CTTCTTGGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
10 20 0.54
11 17 0.46
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (10 bp):
TCATTTTGAG
Found at i:1320370 original size:21 final size:21
Alignment explanation
Indices: 1320344--1320402 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
1320334 TAACTGAAAC
*
1320344 ATCATTTTGAGTCATTTTCGA
1 ATCATTTTGAGTCACTTTCGA
1320365 ATCATTTTGAGTCACTTTCGA
1 ATCATTTTGAGTCACTTTCGA
1320386 ATCATTTTGAGTCACTT
1 ATCATTTTGAGTCACTT
1320403 CTTGGGTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.46
Consensus pattern (21 bp):
ATCATTTTGAGTCACTTTCGA
Found at i:1322821 original size:27 final size:27
Alignment explanation
Indices: 1322790--1322846 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
1322780 GTATGGGGTA
* **
1322790 GGTGGCGCCTATCTGGTAGGCGCGACT
1 GGTGGAGCCTATCTGACAGGCGCGACT
1322817 GGTGGAGCCTATCTGACAGGCGCGACT
1 GGTGGAGCCTATCTGACAGGCGCGACT
1322844 GGT
1 GGT
1322847 TGAACAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.14, C:0.25, G:0.40, T:0.21
Consensus pattern (27 bp):
GGTGGAGCCTATCTGACAGGCGCGACT
Found at i:1323050 original size:59 final size:59
Alignment explanation
Indices: 1322987--1323100 Score: 201
Period size: 59 Copynumber: 1.9 Consensus size: 59
1322977 ATACTAAACT
* *
1322987 AAACACAACAATTTATAACATTATCCTAAATTACTAATAAATTAATTTTAAAATATTAC
1 AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATATTAC
*
1323046 AAACACAACAATTTATACCATAATCCTAAATTACTAACAAATTAATTTTAAAATA
1 AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATA
1323101 ATTATAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (59 bp):
AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATATTAC
Found at i:1323279 original size:27 final size:27
Alignment explanation
Indices: 1323241--1323294 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1323231 AAGGGAGAGG
*
1323241 CAGTGGCGCCTACCTGTCAGGCGTGAC
1 CAGTGGCGCCTACCTGACAGGCGTGAC
* *
1323268 CAGTGGTGCCTATCTGACAGGCGTGAC
1 CAGTGGCGCCTACCTGACAGGCGTGAC
1323295 TGGTCTTGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.30, G:0.33, T:0.20
Consensus pattern (27 bp):
CAGTGGCGCCTACCTGACAGGCGTGAC
Found at i:1348871 original size:190 final size:189
Alignment explanation
Indices: 1348520--1348879 Score: 510
Period size: 190 Copynumber: 1.9 Consensus size: 189
1348510 CTTTAAAATT
* * * * * *
1348520 TTTAAAATTTTAAATTAATAAAGATAAATTTATATTTTGACTCCCCTAAAAATATAAAAATTTGA
1 TTTAAAATTTCAAATTAATAAAGATAAAATTACACTTTGA-GCCCCTAAAAACATAAAAATTTGA
*
1348585 TTTAATACTTTAAAATTATAAAGATATAAGCTATTAAGATGGTGAAATTACATTTTTATTATCGT
65 TTTAATACTTTAAAATTATAAAGATATAAGCTATTAAAATGGTGAAATTACATTTTTATTATCGT
* **
1348650 AAAAATTACAATTTAATTTTGGCCACCCCTAAAAAAAATTCTGGTTTCACCCCGGCCCCC
130 AAAAATCACAATTTAATTTAAGCCACCCCTAAAAAAAATTCTGGTTTCACCCCGGCCCCC
*
1348710 TTTAAAATTTCAAATTAATAAAGGTAAAATTACACTTTG-GCCCCTAAAAACATAAAAATTTGAT
1 TTTAAAATTTCAAATTAATAAAGATAAAATTACACTTTGAGCCCCTAAAAACATAAAAATTTGAT
* * *
1348774 TTAATCCTTTAAAAATTATAAAGATATAGGCTATTAAAATGGTGAAATTATATTTTT-TGCTATC
66 TTAATACTTT-AAAATTATAAAGATATAAGCTATTAAAATGGTGAAATTACATTTTTAT--TATC
* *
1348838 TTAAAAATCACAATTTAATTTCAATCC-CCCCTAAAAAAAATT
128 GTAAAAATCACAATTTAATTT-AAGCCACCCCTAAAAAAAATT
1348880 TTGATTTTGC
Statistics
Matches: 150, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
188 33 0.22
189 43 0.29
190 72 0.48
191 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (189 bp):
TTTAAAATTTCAAATTAATAAAGATAAAATTACACTTTGAGCCCCTAAAAACATAAAAATTTGAT
TTAATACTTTAAAATTATAAAGATATAAGCTATTAAAATGGTGAAATTACATTTTTATTATCGTA
AAAATCACAATTTAATTTAAGCCACCCCTAAAAAAAATTCTGGTTTCACCCCGGCCCCC
Found at i:1357609 original size:20 final size:21
Alignment explanation
Indices: 1357586--1357633 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
1357576 ATACACATTA
*
1357586 AAATATATATAAA-TCAAAAT
1 AAATATATAAAAATTCAAAAT
1357606 AAATATATAAAAATTCAAAA-
1 AAATATATAAAAATTCAAAAT
1357626 AACATATA
1 AA-ATATA
1357634 AAATTTAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATATATAAAAATTCAAAAT
Found at i:1357634 original size:19 final size:21
Alignment explanation
Indices: 1357610--1357656 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
1357600 CAAAATAAAT
1357610 ATATAAAAATT-CAAAA-AAC
1 ATATAAAAATTACAAAACAAC
* *
1357629 ATATAAAATTTAGAAAACAAC
1 ATATAAAAATTACAAAACAAC
1357650 ATATAAA
1 ATATAAA
1357657 TTATAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.42
20 4 0.17
21 10 0.42
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (21 bp):
ATATAAAAATTACAAAACAAC
Found at i:1357666 original size:21 final size:20
Alignment explanation
Indices: 1357622--1357666 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1357612 ATAAAAATTC
1357622 AAAAAACATATAAAATTTAGA
1 AAAAAACATATAAAATTTA-A
*
1357643 AAACAACATAT-AAATTATAA
1 AAAAAACATATAAAATT-TAA
1357663 AAAA
1 AAAA
1357667 TTATAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.22
Consensus pattern (20 bp):
AAAAAACATATAAAATTTAA
Found at i:1357676 original size:19 final size:17
Alignment explanation
Indices: 1357610--1357680 Score: 54
Period size: 19 Copynumber: 3.9 Consensus size: 17
1357600 CAAAATAAAT
1357610 ATATAAAAATTCAAAAAA
1 ATATAAAAATT-AAAAAA
*
1357628 CATATAAAATTTAGAAAACA
1 -ATATAAAAATTA-AAAA-A
* *
1357648 ACATATAAATTATAAAAA
1 ATATAAAAATTA-AAAAA
1357666 ATTATAAAAA-TAAAA
1 A-TATAAAAATTAAAA
1357681 TTACAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
17 3 0.07
18 5 0.12
19 33 0.79
20 1 0.02
ACGTcount: A:0.68, C:0.06, G:0.01, T:0.25
Consensus pattern (17 bp):
ATATAAAAATTAAAAAA
Found at i:1357750 original size:8 final size:9
Alignment explanation
Indices: 1357734--1357821 Score: 63
Period size: 9 Copynumber: 9.6 Consensus size: 9
1357724 AATAATATTA
1357734 TAAACAATA-
1 TAAA-AATAT
1357743 TAAAAATATT
1 TAAAAATA-T
* *
1357753 TTAAAATTT
1 TAAAAATAT
*
1357762 TAAAAATAG
1 TAAAAATAT
*
1357771 TAAAAATAG
1 TAAAAATAT
1357780 TAAAAATAATT
1 TAAAAAT-A-T
* *
1357791 TAAAACTTT
1 TAAAAATAT
*
1357800 TAAAAATAA
1 TAAAAATAT
1357809 TAAAAA-AT
1 TAAAAATAT
1357817 TAAAA
1 TAAAA
1357822 TTAAAATTAA
Statistics
Matches: 63, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
8 10 0.16
9 40 0.63
10 7 0.11
11 6 0.10
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (9 bp):
TAAAAATAT
Found at i:1357793 original size:37 final size:37
Alignment explanation
Indices: 1357733--1357822 Score: 121
Period size: 37 Copynumber: 2.4 Consensus size: 37
1357723 TAATAATATT
*
1357733 ATAAACAATATAAAAATATTTTAAAA-TTTTAAAAATA
1 ATAAA-AATATAAAAATAATTTAAAACTTTTAAAAATA
*
1357770 GTAAAAATAGTAAAAATAATTTAAAACTTTTAAAAATA
1 ATAAAAATA-TAAAAATAATTTAAAACTTTTAAAAATA
*
1357808 ATAAAAA-ATTAAAAT
1 ATAAAAATATAAAAAT
1357823 TAAAATTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
36 10 0.21
37 20 0.43
38 17 0.36
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (37 bp):
ATAAAAATATAAAAATAATTTAAAACTTTTAAAAATA
Found at i:1357919 original size:39 final size:40
Alignment explanation
Indices: 1357818--1357910 Score: 143
Period size: 39 Copynumber: 2.3 Consensus size: 40
1357808 ATAAAAAATT
1357818 AAAATTAAAATTAAAAAATATGTTATTTATAAGTTTTTAATA
1 AAAATTAAAATTAAAAAATA--TTATTTATAAGTTTTTAATA
* *
1357860 AAATTTAAAATTAAAAAATATTATTTAT-ATTTTTTAATA
1 AAAATTAAAATTAAAAAATATTATTTATAAGTTTTTAATA
1357899 AAAATTAAAATT
1 AAAATTAAAATT
1357911 TTTAAATATA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 21 0.44
40 8 0.17
42 19 0.40
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (40 bp):
AAAATTAAAATTAAAAAATATTATTTATAAGTTTTTAATA
Found at i:1358733 original size:19 final size:19
Alignment explanation
Indices: 1358705--1358741 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1358695 AGTTTAATGT
* *
1358705 TTAATTAATTAAGTTTTAA
1 TTAATCAATTAAGATTTAA
1358724 TTAATCAATTAAGATTTA
1 TTAATCAATTAAGATTTA
1358742 CTAAGTTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (19 bp):
TTAATCAATTAAGATTTAA
Found at i:1362298 original size:30 final size:30
Alignment explanation
Indices: 1362262--1362358 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
1362252 CAAGATAAAA
*
1362262 ATTAAATCAAATTTAATAACTCATATTAAT
1 ATTAAATCAAATTTAATAACTCACATTAAT
* ** * *
1362292 ATTAAAT-TAATAAAAT-ACTATCAAGATAAAT
1 ATTAAATCAAATTTAATAAC--TC-ACATTAAT
1362323 ATTAAATCAAATTTAATAACTCACATTAAT
1 ATTAAATCAAATTTAATAACTCACATTAAT
1362353 ATTAAA
1 ATTAAA
1362359 GTAATAAAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
28 2 0.04
29 6 0.12
30 21 0.40
31 15 0.29
32 6 0.12
33 2 0.04
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.36
Consensus pattern (30 bp):
ATTAAATCAAATTTAATAACTCACATTAAT
Found at i:1362300 original size:61 final size:61
Alignment explanation
Indices: 1362225--1362401 Score: 309
Period size: 61 Copynumber: 2.9 Consensus size: 61
1362215 AATTACTTAG
*
1362225 ATTAATATTAAATTAATAAAATACTATCAAGATAAAAATTAAATCAAATTTAATAACTCAT
1 ATTAATATTAAATTAATAAAATACTATCAAGATAAAAATTAAATCAAATTTAATAACTCAC
*
1362286 ATTAATATTAAATTAATAAAATACTATCAAGATAAATATTAAATCAAATTTAATAACTCAC
1 ATTAATATTAAATTAATAAAATACTATCAAGATAAAAATTAAATCAAATTTAATAACTCAC
* * *
1362347 ATTAATATTAAAGTAATAAAATACTATCAAGATAAAAATTAAATTAAATTAAATA
1 ATTAATATTAAATTAATAAAATACTATCAAGATAAAAATTAAATCAAATTTAATA
1362402 TTAAATTTAT
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 110 1.00
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.34
Consensus pattern (61 bp):
ATTAATATTAAATTAATAAAATACTATCAAGATAAAAATTAAATCAAATTTAATAACTCAC
Found at i:1362417 original size:17 final size:18
Alignment explanation
Indices: 1362379--1362418 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1362369 ACTATCAAGA
1362379 TAAAA-ATTAAATTAAAT
1 TAAAATATTAAATTAAAT
*
1362396 T-AAATATTAAATT-TAT
1 TAAAATATTAAATTAAAT
1362412 TAAAATA
1 TAAAATA
1362419 ATATTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAATATTAAATTAAAT
Found at i:1374615 original size:20 final size:20
Alignment explanation
Indices: 1374599--1374678 Score: 76
Period size: 19 Copynumber: 4.0 Consensus size: 20
1374589 ATCAAAAATT
1374599 TATTTTAAAAATTAAAAAAA
1 TATTTTAAAAATTAAAAAAA
1374619 TATTTT-AAAATTAAAAAAA
1 TATTTTAAAAATTAAAAAAA
*** **
1374638 TA-AAAAAAAGTATTTTAAAAA
1 TATTTTAAAA--ATTAAAAAAA
1374659 TATTTT-AAAATTAAAAAAA
1 TATTTTAAAAATTAAAAAAA
1374678 T
1 T
1374679 TAAAAAAATA
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
19 27 0.59
20 6 0.13
21 13 0.28
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (20 bp):
TATTTTAAAAATTAAAAAAA
Found at i:1374674 original size:17 final size:17
Alignment explanation
Indices: 1374652--1374698 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
1374642 AAAAAGTATT
*
1374652 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
* *
1374669 TTAAAAAAATTAAAAAA
1 TTAAAAATATTTAAAAA
*
1374686 ATAAAAATATTTA
1 TTAAAAATATTTA
1374699 TTATATATGG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:1378017 original size:15 final size:15
Alignment explanation
Indices: 1377997--1378026 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1377987 TAAATATTTT
1377997 TTAAAAATATTTACG
1 TTAAAAATATTTACG
1378012 TTAAAAATATTTACG
1 TTAAAAATATTTACG
1378027 AAGCTAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (15 bp):
TTAAAAATATTTACG
Found at i:1378307 original size:6 final size:6
Alignment explanation
Indices: 1378289--1378376 Score: 72
Period size: 6 Copynumber: 14.3 Consensus size: 6
1378279 ACAAATAAAT
* * * *
1378289 AAAAGA AATAGA AAAAGA AAAAGAA ACAAAGCA AAACGA AACAG- GAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAG-A A-AAAG-A AAAAGA AAAAGA AAAAGA
* *
1378339 AAAAGA AAAAG- GAAAGA AAAAGA GAAAGA AGAAAGA AA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA A-AAAGA AA
1378377 GTCACGGCCT
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
5 7 0.11
6 40 0.62
7 11 0.17
8 6 0.09
ACGTcount: A:0.74, C:0.05, G:0.20, T:0.01
Consensus pattern (6 bp):
AAAAGA
Found at i:1378346 original size:17 final size:17
Alignment explanation
Indices: 1378302--1378361 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
1378292 AGAAATAGAA
1378302 AAAGAAAAAGAAAC---
1 AAAGAAAAAGAAACAGG
*
1378316 AAAGCAAAACGAAACAGG
1 AAAG-AAAAAGAAACAGG
*
1378334 AAAGAAAAAGAAAAAGG
1 AAAGAAAAAGAAACAGG
1378351 AAAGAAAAAGA
1 AAAGAAAAAGA
1378362 GAAAGAAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
14 4 0.10
15 9 0.23
17 22 0.56
18 4 0.10
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGAAACAGG
Found at i:1378354 original size:11 final size:11
Alignment explanation
Indices: 1378340--1378377 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
1378330 CAGGAAAGAA
1378340 AAAGAAAAAGG
1 AAAGAAAAAGG
1378351 AAAGAAAAAGAG
1 AAAGAAAAAG-G
1378363 AAAGAAGAAA-G
1 AAAGAA-AAAGG
1378374 AAAG
1 AAAG
1378378 TCACGGCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 15 0.60
12 7 0.28
13 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAGG
Found at i:1378366 original size:17 final size:17
Alignment explanation
Indices: 1378316--1378376 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
1378306 AAAAAGAAAC
* *
1378316 AAAGCAAAACGAAACAGG
1 AAAG-AAAAAGAAAAAGG
1378334 AAAGAAAAAGAAAAAGG
1 AAAGAAAAAGAAAAAGG
*
1378351 AAAGAAAAAGAGAAAGAAG
1 AAAGAAAAAGA-AAA-AGG
1378370 AAAGAAA
1 AAAGAAA
1378377 GTCACGGCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
17 22 0.58
18 7 0.18
19 9 0.24
ACGTcount: A:0.72, C:0.05, G:0.23, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGAAAAAGG
Found at i:1379299 original size:41 final size:40
Alignment explanation
Indices: 1379254--1379370 Score: 107
Period size: 41 Copynumber: 3.0 Consensus size: 40
1379244 TGACTTCGAG
1379254 TCGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAA
1 TCGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAA
* ** *
1379294 TTCGATGAGGCTTTGGGTG-CTAATTTACT--TT-GGTTTAA
1 -TCGATGAGACACTGGGTGTC-AATTTACTACTTCGGATTAA
* * * * *
1379332 CCGATGAGAGACTGTGTGTCAATTTATTACTTCGAATTA
1 TCGATGAGACACTGGGTGTCAATTTACTACTTCGGATTA
1379371 TCTGATCAGG
Statistics
Matches: 58, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
37 19 0.33
38 7 0.12
39 4 0.07
40 5 0.09
41 23 0.40
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAA
Done.