Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007418.1 Hibiscus syriacus cultivar Beakdansim tig00020063_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1198774
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:1001 original size:7 final size:7
Alignment explanation
Indices: 989--1097 Score: 75
Period size: 8 Copynumber: 15.1 Consensus size: 7
979 CTTTTTTTCA
989 TCATTTT
1 TCATTTT
996 TCA--TT
1 TCATTTT
1001 TCATTTTT
1 TCA-TTTT
1009 TCATTTTT
1 TCA-TTTT
1017 TCATTTTT
1 TCA-TTTT
1025 TCATTTTT
1 TCA-TTTT
1033 TCATTTT
1 TCATTTT
1040 TCCCATTTT
1 T--CATTTT
1049 TCA-TTT
1 TCATTTT
1055 TCA-TTT
1 TCATTTT
*
1061 TC-CTTT
1 TCATTTT
*
1067 TCCTTTT
1 TCATTTT
*
1074 TCCTTTT
1 TCATTTT
*
1081 TATATTTT
1 T-CATTTT
1089 TCTATTTT
1 TC-ATTTT
1097 T
1 T
1098 TCACTTCTTC
Statistics
Matches: 89, Mismatches: 4, Indels: 17
0.81 0.04 0.15
Matches are distributed among these distances:
5 5 0.06
6 16 0.18
7 21 0.24
8 40 0.45
9 7 0.08
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (7 bp):
TCATTTT
Found at i:1004 original size:12 final size:13
Alignment explanation
Indices: 981--1030 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 13
971 TTATTCTTCT
981 TTTTTTCA--TCA
1 TTTTTTCATTTCA
992 -TTTTTCATTTCA
1 TTTTTTCATTTCA
1004 TTTTTTCATTTTTTCA
1 TTTTTTCA---TTTCA
1020 TTTTTTCATTT
1 TTTTTTCATTT
1031 TTTCATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
10 7 0.21
12 3 0.09
13 10 0.30
16 13 0.39
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTCATTTCA
Found at i:1007 original size:21 final size:21
Alignment explanation
Indices: 983--1022 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
973 ATTCTTCTTT
983 TTTTCATCA-TTTTTCATTTCA
1 TTTT-ATCATTTTTTCATTTCA
*
1004 TTTTTTCATTTTTTCATTT
1 TTTTATCATTTTTTCATTT
1023 TTTCATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTATCATTTTTTCATTTCA
Found at i:1012 original size:8 final size:8
Alignment explanation
Indices: 999--1055 Score: 89
Period size: 8 Copynumber: 7.1 Consensus size: 8
989 TCATTTTTCA
999 TTTCATTT
1 TTTCATTT
1007 TTTCATTT
1 TTTCATTT
1015 TTTCATTT
1 TTTCATTT
1023 TTTCATTT
1 TTTCATTT
1031 TTTCATTT
1 TTTCATTT
*
1039 TTCCCA-TT
1 TT-TCATTT
1047 TTTCATTT
1 TTTCATTT
1055 T
1 T
1056 CATTTTCCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
7 2 0.04
8 41 0.91
9 2 0.04
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTCATTT
Found at i:4654 original size:33 final size:33
Alignment explanation
Indices: 4612--4678 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
4602 CTTAGTACAG
4612 ATGGTGGACACGACCTTATATGTCATACGGATT
1 ATGGTGGACACGACCTTATATGTCATACGGATT
*
4645 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATATGTCATACGGATT
4678 A
1 A
4679 GCACTACGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (33 bp):
ATGGTGGACACGACCTTATATGTCATACGGATT
Found at i:6806 original size:33 final size:34
Alignment explanation
Indices: 6764--6830 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
6754 CATTTTTGAA
6764 ATCAATTTTGAAAA-TACTCCCCCTTACTTTATT
1 ATCAATTTTGAAAATTACTCCCCCTTACTTTATT
*
6797 ATCAATTTTGAAAATTACTCCCCCTTGCTTTATT
1 ATCAATTTTGAAAATTACTCCCCCTTACTTTATT
6831 CTCCCCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 14 0.44
34 18 0.56
ACGTcount: A:0.28, C:0.24, G:0.04, T:0.43
Consensus pattern (34 bp):
ATCAATTTTGAAAATTACTCCCCCTTACTTTATT
Found at i:8667 original size:18 final size:17
Alignment explanation
Indices: 8646--8679 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
8636 CAACATAATT
8646 AAATAAAAAATAATTTTA
1 AAAT-AAAAATAATTTTA
*
8664 AAATCAAAATAATTTT
1 AAATAAAAATAATTTT
8680 TTTATTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATAAAAATAATTTTA
Found at i:31475 original size:2 final size:2
Alignment explanation
Indices: 31468--31494 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31458 TTGTTCGACA
31468 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
31495 GCTTGGTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52067 original size:20 final size:20
Alignment explanation
Indices: 52039--52096 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 20
52029 AAGGAAAAAT
* *
52039 AAAATAAAAATAAAAGAGGA
1 AAAAGAAAAATAAAAGAGAA
*
52059 AAAAGAAAAAGAAAAAGAGAA
1 AAAAGAAAAA-TAAAAGAGAA
52080 AAAAGAAAAATAAAAGA
1 AAAAGAAAAATAAAAGA
52097 AATGTCCAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (20 bp):
AAAAGAAAAATAAAAGAGAA
Found at i:53033 original size:20 final size:19
Alignment explanation
Indices: 53000--53049 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
52990 CCATCTTGGA
*
53000 CCTTTTTTATTTTTATTTTT
1 CCTTTTTT-CTTTTATTTTT
*
53020 TCTCTTTTTCTTTTATTTTT
1 CCT-TTTTTCTTTTATTTTT
53040 CCTTTTTTCT
1 CCTTTTTTCT
53050 CTTTTCTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 7 0.27
20 14 0.54
21 5 0.19
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (19 bp):
CCTTTTTTCTTTTATTTTT
Found at i:53033 original size:26 final size:28
Alignment explanation
Indices: 53004--53064 Score: 99
Period size: 27 Copynumber: 2.2 Consensus size: 28
52994 CTTGGACCTT
53004 TTTTATTTTT-ATTTTTTCTCTTTT-TC
1 TTTTATTTTTCATTTTTTCTCTTTTCTC
*
53030 TTTTATTTTTCCTTTTTTCTCTTTTCTC
1 TTTTATTTTTCATTTTTTCTCTTTTCTC
53058 TTTTATT
1 TTTTATT
53065 AAAATTTTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 10 0.31
27 13 0.41
28 9 0.28
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.79
Consensus pattern (28 bp):
TTTTATTTTTCATTTTTTCTCTTTTCTC
Found at i:53072 original size:27 final size:27
Alignment explanation
Indices: 53014--53072 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
53004 TTTTATTTTT
***
53014 ATTTTTTCTCTTTTTCTTTTATTTTTC
1 ATTTTTTCTCTTTTTCTTTTATTTAAA
*
53041 CTTTTTTCTCTTTTCTCTTTTA-TTAAA
1 ATTTTTTCTCTTTT-TCTTTTATTTAAA
53068 ATTTT
1 ATTTT
53073 CCTTTTCTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (27 bp):
ATTTTTTCTCTTTTTCTTTTATTTAAA
Found at i:53953 original size:64 final size:61
Alignment explanation
Indices: 53884--54062 Score: 189
Period size: 64 Copynumber: 2.8 Consensus size: 61
53874 TGGGACACTT
* *
53884 AGTGCATCGGTGCACTAAGGATGCATCTATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTG
1 AGTGCATCGATGCA-T--GGATGCATCGATGCATAAAATGCATTCGATGTTTG-AAAATAGCCTG
* * **
53949 -GTGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTCTG
1 AGTGCATCGATGCATGG---ATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAGCCTG
* *
54012 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCAT-G-GA-TGCATCGATGCATAAAATGCATTCGATGTT
54063 CAATTAAATC
Statistics
Matches: 98, Mismatches: 9, Indels: 15
0.80 0.07 0.12
Matches are distributed among these distances:
61 2 0.02
63 10 0.10
64 84 0.86
65 1 0.01
66 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (61 bp):
AGTGCATCGATGCATGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAGCCTG
Found at i:54090 original size:64 final size:63
Alignment explanation
Indices: 53905--54062 Score: 199
Period size: 64 Copynumber: 2.5 Consensus size: 63
53895 GCACTAAGGA
* * * ** ***
53905 TGCATCTATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATCAAATGCATTCGATGTTT-CAAAATATTCTGGTGCATCGATGCATGGAGAG
*
53969 TGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTCTGAGTGCATCGATGCATGGAGAG
1 TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATTCTG-GTGCATCGATGCATGGAGAG
* *
54033 TGCATCGGTGCATGAAATGCATTCGATGTT
1 TGCATCGATGCATCAAATGCATTCGATGTT
54063 CAATTAAATC
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 9 0.11
64 74 0.89
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (63 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATTCTGGTGCATCGATGCATGGAGAG
Found at i:56687 original size:28 final size:28
Alignment explanation
Indices: 56651--56749 Score: 119
Period size: 29 Copynumber: 3.5 Consensus size: 28
56641 TATGGTGGTA
56651 TTTTGTAAATATTGTTAAAAAATATTAG
1 TTTTGTAAATATTGTTAAAAAATATTAG
*
56679 TTTCGTAAATATTGTTAAAAAA-ATGATAG
1 TTTTGTAAATATTGTTAAAAAATAT--TAG
* ** *
56708 TTTTGTAAGTATTGTTAAGAAGGTGTTAG
1 TTTTGTAAATATTGTTAA-AAAATATTAG
56737 TTTTGTAAATATT
1 TTTTGTAAATATT
56750 TTGAGAAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 21 0.35
29 34 0.57
30 2 0.03
31 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.16, T:0.45
Consensus pattern (28 bp):
TTTTGTAAATATTGTTAAAAAATATTAG
Found at i:56709 original size:29 final size:29
Alignment explanation
Indices: 56651--56851 Score: 123
Period size: 28 Copynumber: 7.0 Consensus size: 29
56641 TATGGTGGTA
56651 TTTTGTAAATATTGTT-AAAAAAT-ATTAG
1 TTTTGTAAATATTGTTAAAAAAATGA-TAG
*
56679 TTTCGTAAATATTGTTAAAAAAATGATAG
1 TTTTGTAAATATTGTTAAAAAAATGATAG
* * ** *
56708 TTTTGTAAGTATTGTTAAGAAGGTGTTAG
1 TTTTGTAAATATTGTTAAAAAAATGATAG
56737 TTTTGTAAATATT-TTGAGAAAAAAAATGATA-
1 TTTTGTAAATATTGTT----AAAAAAATGATAG
* * *
56768 TTTTGGTAATTATT-TCAAAAAAGTGATA-
1 TTTT-GTAAATATTGTTAAAAAAATGATAG
* ** *
56796 TTTTGGTAATTATT-TCGAAAAAGTGATA-
1 TTTT-GTAAATATTGTTAAAAAAATGATAG
* * *
56824 TTTTGGTAATTATT-TCAAAAAAGTGATA
1 TTTT-GTAAATATTGTTAAAAAAATGATA
56852 ATTCGAAAAA
Statistics
Matches: 149, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
28 82 0.55
29 45 0.30
30 1 0.01
31 4 0.03
32 17 0.11
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (29 bp):
TTTTGTAAATATTGTTAAAAAAATGATAG
Found at i:56788 original size:28 final size:28
Alignment explanation
Indices: 56756--56851 Score: 174
Period size: 28 Copynumber: 3.4 Consensus size: 28
56746 TATTTTGAGA
*
56756 AAAAAAATGATATTTTGGTAATTATTTC
1 AAAAAAGTGATATTTTGGTAATTATTTC
56784 AAAAAAGTGATATTTTGGTAATTATTTC
1 AAAAAAGTGATATTTTGGTAATTATTTC
*
56812 GAAAAAGTGATATTTTGGTAATTATTTC
1 AAAAAAGTGATATTTTGGTAATTATTTC
56840 AAAAAAGTGATA
1 AAAAAAGTGATA
56852 ATTCGAAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 65 1.00
ACGTcount: A:0.43, C:0.03, G:0.15, T:0.40
Consensus pattern (28 bp):
AAAAAAGTGATATTTTGGTAATTATTTC
Found at i:56857 original size:44 final size:46
Alignment explanation
Indices: 56809--56897 Score: 164
Period size: 44 Copynumber: 2.0 Consensus size: 46
56799 TGGTAATTAT
56809 TTCGAAAAAGTGATATTTTGGTAATTATTTC-AAAAAA-GTGATAA
1 TTCGAAAAAGTGATATTTTGGTAATTATTTCGAAAAAAGGTGATAA
56853 TTCGAAAAAGTGATATTTTGGTAATTATTTCGAAAAAAGGTGATA
1 TTCGAAAAAGTGATATTTTGGTAATTATTTCGAAAAAAGGTGATA
56898 TTTTCGTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 31 0.72
45 6 0.14
46 6 0.14
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.36
Consensus pattern (46 bp):
TTCGAAAAAGTGATATTTTGGTAATTATTTCGAAAAAAGGTGATAA
Found at i:56898 original size:30 final size:28
Alignment explanation
Indices: 56853--56911 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 28
56843 AAAGTGATAA
*
56853 TTCGAAAAAGTGATATTTTGGTAATTAT
1 TTCGAAAAAGTGATATTTTCGTAATTAT
56881 TTCGAAAAAAGGTGATATTTTCGTAATTAT
1 TTCG-AAAAA-GTGATATTTTCGTAATTAT
56911 T
1 T
56912 AAAAACAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 4 0.14
29 5 0.18
30 19 0.68
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (28 bp):
TTCGAAAAAGTGATATTTTCGTAATTAT
Found at i:61062 original size:28 final size:28
Alignment explanation
Indices: 61026--61120 Score: 131
Period size: 28 Copynumber: 3.5 Consensus size: 28
61016 TATGGTGGTA
61026 TTTTGTAAATATTGTTAAAAAATGTTAG
1 TTTTGTAAATATTGTTAAAAAATGTTAG
* *
61054 TTTCGTAAATATTGTTAAAAAATGATAG
1 TTTTGTAAATATTGTTAAAAAATGTTAG
* **
61082 TTTTGTAAGTATTGTT--AAGGTGTTAG
1 TTTTGTAAATATTGTTAAAAAATGTTAG
61108 TTTTGTAAATATT
1 TTTTGTAAATATT
61121 TTGAGAAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
26 19 0.32
28 40 0.68
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.47
Consensus pattern (28 bp):
TTTTGTAAATATTGTTAAAAAATGTTAG
Found at i:61151 original size:30 final size:29
Alignment explanation
Indices: 61108--61178 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
61098 AAGGTGTTAG
*
61108 TTTT-GTAAATATTTTGAGAAAAAATGATA
1 TTTTGGTAATTATTTT-AGAAAAAATGATA
* *
61137 TTTTGGTAATTA-TTTCGAAAAAGTGATA
1 TTTTGGTAATTATTTTAGAAAAAATGATA
61165 -TTTGGTAATTATTT
1 TTTTGGTAATTATTT
61179 CAAAAAAGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 11 0.30
28 13 0.35
29 7 0.19
30 6 0.16
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.46
Consensus pattern (29 bp):
TTTTGGTAATTATTTTAGAAAAAATGATA
Found at i:61158 original size:27 final size:27
Alignment explanation
Indices: 61126--61188 Score: 101
Period size: 27 Copynumber: 2.3 Consensus size: 27
61116 ATATTTTGAG
61126 AAAAAA-TGATATTTTGGTAATTATTTC
1 AAAAAAGTGATA-TTTGGTAATTATTTC
*
61153 GAAAAAGTGATATTTGGTAATTATTTC
1 AAAAAAGTGATATTTGGTAATTATTTC
61180 AAAAAAGTG
1 AAAAAAGTG
61189 TTAATTCGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 28 0.85
28 5 0.15
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (27 bp):
AAAAAAGTGATATTTGGTAATTATTTC
Found at i:61198 original size:43 final size:44
Alignment explanation
Indices: 61150--61232 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
61140 TGGTAATTAT
61150 TTCGAAAAAGTGATA-TTTGGTAATTATTTCAAAAAAGTGTTAA
1 TTCGAAAAAGTGATATTTTGGTAATTATTTCAAAAAAGTGTTAA
*
61193 TTCGAAAAAGTGATATTTTGGTAATTATTTCGAAAAAGTG
1 TTCGAAAAAGTGATATTTTGGTAATTATTTCAAAAAAGTG
61233 ATATTTTCGT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
43 15 0.39
44 23 0.61
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.37
Consensus pattern (44 bp):
TTCGAAAAAGTGATATTTTGGTAATTATTTCAAAAAAGTGTTAA
Found at i:61233 original size:28 final size:28
Alignment explanation
Indices: 61193--61272 Score: 108
Period size: 28 Copynumber: 2.9 Consensus size: 28
61183 AAAGTGTTAA
*
61193 TTCGAAAAAGTGATATTTTGGTAATTAT
1 TTCGAAAAAGTGATATTTTCGTAATTAT
61221 TTCGAAAAAGTGATATTTTCGTAATTA-
1 TTCGAAAAAGTGATATTTTCGTAATTAT
** * *
61248 TTAAAAAAAATGTTATTTTCGTAAT
1 TTCGAAAAAGTGATATTTTCGTAAT
61273 AGTTGAATGT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 21 0.45
28 26 0.55
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (28 bp):
TTCGAAAAAGTGATATTTTCGTAATTAT
Found at i:61255 original size:71 final size:71
Alignment explanation
Indices: 61125--61262 Score: 224
Period size: 71 Copynumber: 1.9 Consensus size: 71
61115 AATATTTTGA
* * *
61125 GAAAAAATGATATTTTGGTAATTATTTCGAAAAAGTGATATTTGGTAATTATTTCAAAAAAGTGT
1 GAAAAAATGATATTTTGGTAATTATTTCGAAAAAGTGATATTTCGTAATTATTTAAAAAAAATGT
61190 TAATTC
66 TAATTC
*
61196 GAAAAAGTGATATTTTGGTAATTATTTCGAAAAAGTGATATTTTCGTAATTA-TTAAAAAAAATG
1 GAAAAAATGATATTTTGGTAATTATTTCGAAAAAGTGATA-TTTCGTAATTATTTAAAAAAAATG
61260 TTA
65 TTA
61263 TTTTCGTAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
71 52 0.84
72 10 0.16
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.39
Consensus pattern (71 bp):
GAAAAAATGATATTTTGGTAATTATTTCGAAAAAGTGATATTTCGTAATTATTTAAAAAAAATGT
TAATTC
Found at i:63025 original size:39 final size:37
Alignment explanation
Indices: 62982--63057 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 37
62972 AAAAGTTAAA
62982 AAAATAATAAAATAA-AATAGATAAAAATAAATAAAAGGG
1 AAAATAAT-AAATAATAATAG-TAAAAAT-AATAAAAGGG
* *
63021 AAAATAATAAATAATAATAGTAATAATTATAAAAGGG
1 AAAATAATAAATAATAATAGTAAAAATAATAAAAGGG
63058 GGGTTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 9 0.26
38 12 0.35
39 13 0.38
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (37 bp):
AAAATAATAAATAATAATAGTAAAAATAATAAAAGGG
Found at i:63045 original size:19 final size:19
Alignment explanation
Indices: 62984--63047 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
62974 AAGTTAAAAA
62984 AATAATAAAATAAAATAGAT
1 AATAAT-AAATAAAATAGAT
* ** *
63004 AAAAATAAATAAAAGGGAA
1 AATAATAAATAAAATAGAT
63023 AATAATAAATAATAATAG-T
1 AATAATAAATAA-AATAGAT
63042 AATAAT
1 AATAAT
63048 TATAAAAGGG
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
19 27 0.77
20 8 0.23
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (19 bp):
AATAATAAATAAAATAGAT
Found at i:64241 original size:9 final size:9
Alignment explanation
Indices: 64227--64310 Score: 69
Period size: 10 Copynumber: 8.8 Consensus size: 9
64217 GGCTGCTGGA
64227 AACCGGTTT
1 AACCGGTTT
64236 AACCGGTTTT
1 AACCGG-TTT
64246 CAACCGGTTT
1 -AACCGGTTT
*
64256 GACCGGTTT
1 AACCGGTTT
*
64265 CAACCGGTTCG
1 -AACCGGTT-T
64276 AACCGGTTT
1 AACCGGTTT
* * *
64285 GACTGGTCTG
1 AACCGGT-TT
64295 AACCGGTTT
1 AACCGGTTT
*
64304 GACCGGT
1 AACCGGT
64311 CTGACCCGAC
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
9 26 0.44
10 27 0.46
11 6 0.10
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:64252 original size:20 final size:20
Alignment explanation
Indices: 64227--64284 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
64217 GGCTGCTGGA
64227 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTAACCGGTTTTC
*
64247 AACCGGTTTGACCGG-TTTC
1 AACCGGTTTAACCGGTTTTC
*
64266 AACCGGTTCGAACCGGTTT
1 AACCGGTT-TAACCGGTTT
64285 GACTGGTCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 12 0.36
20 19 0.58
21 2 0.06
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (20 bp):
AACCGGTTTAACCGGTTTTC
Found at i:64272 original size:10 final size:10
Alignment explanation
Indices: 64227--64284 Score: 68
Period size: 9 Copynumber: 5.9 Consensus size: 10
64217 GGCTGCTGGA
64227 AACCGGTTT-
1 AACCGGTTTC
64236 AACCGGTTTTC
1 AACCGG-TTTC
64247 AACCGGTTT-
1 AACCGGTTTC
*
64256 GACCGGTTTC
1 AACCGGTTTC
64266 AACCGG-TTC
1 AACCGGTTTC
64275 GAACCGGTTT
1 -AACCGGTTT
64285 GACTGGTCTG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 17 0.40
10 17 0.40
11 8 0.19
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (10 bp):
AACCGGTTTC
Found at i:64279 original size:29 final size:28
Alignment explanation
Indices: 64228--64316 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 28
64218 GCTGCTGGAA
64228 ACCGGTTTAACCGGTTTTC-AACCGGTTTG
1 ACCGGTTTAACCGG--TTCGAACCGGTTTG
64257 ACCGGTTTCAACCGGTTCGAACCGGTTTG
1 ACCGGTTT-AACCGGTTCGAACCGGTTTG
* * * *
64286 ACTGGTCTGAACCGGTTTG-ACCGGTCTG
1 ACCGGT-TTAACCGGTTCGAACCGGTTTG
64314 ACC
1 ACC
64317 CGACCCGACC
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
28 13 0.25
29 32 0.62
30 7 0.13
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (28 bp):
ACCGGTTTAACCGGTTCGAACCGGTTTG
Found at i:64299 original size:19 final size:19
Alignment explanation
Indices: 64248--64314 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
64238 CCGGTTTTCA
* *
64248 ACCGGTTTG-ACCGGTTTCA
1 ACCGGTCTGAACCGGTTT-G
64267 ACCGGT-TCGAACCGGTTTG
1 ACCGGTCT-GAACCGGTTTG
*
64286 ACTGGTCTGAACCGGTTTG
1 ACCGGTCTGAACCGGTTTG
64305 ACCGGTCTGA
1 ACCGGTCTGA
64315 CCCGACCCGA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 1 0.02
19 32 0.76
20 9 0.21
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.28
Consensus pattern (19 bp):
ACCGGTCTGAACCGGTTTG
Found at i:64334 original size:17 final size:17
Alignment explanation
Indices: 64312--64350 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
64302 TTGACCGGTC
64312 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
64329 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
64346 TGACC
1 TGACC
64351 GTTGACCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:71545 original size:5 final size:5
Alignment explanation
Indices: 71535--71587 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
71525 AAACCGGTCT
* *
71535 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
71584 GACC
1 GACC
71588 GTTGACCGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.08
Consensus pattern (5 bp):
GACCC
Found at i:71556 original size:17 final size:17
Alignment explanation
Indices: 71534--71594 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
71524 GAAACCGGTC
71534 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
71551 TGACCCGACCCGACCCGACCGT
1 T-----GACCCGACCCGACCGT
71573 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
71590 TGACC
1 TGACC
71595 GTTGACCGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 22 0.56
22 17 0.44
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.11
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:71560 original size:22 final size:22
Alignment explanation
Indices: 71535--71601 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
71525 AAACCGGTCT
71535 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
71557 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
71579 GACCCGACCGTTGACCGTTGACC
1 GACCCGACC--CGACCGTTGACC
71602 GTTGACCGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 31 0.74
24 11 0.26
ACGTcount: A:0.18, C:0.46, G:0.24, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:71594 original size:7 final size:7
Alignment explanation
Indices: 71584--71614 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
71574 GACCCGACCC
71584 GACCGTT
1 GACCGTT
71591 GACCGTT
1 GACCGTT
71598 GACCGTT
1 GACCGTT
71605 GACCGTT
1 GACCGTT
71612 GAC
1 GAC
71615 TTTCTTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:75102 original size:13 final size:13
Alignment explanation
Indices: 75071--75108 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
75061 TGAAAAATCC
75071 AAGAAAAATAAA-
1 AAGAAAAATAAAT
*
75083 AACAAAAATAAAT
1 AAGAAAAATAAAT
*
75096 CAGAAAAATAAAT
1 AAGAAAAATAAAT
75109 TTGCAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.13
Consensus pattern (13 bp):
AAGAAAAATAAAT
Found at i:78898 original size:74 final size:76
Alignment explanation
Indices: 78777--78990 Score: 321
Period size: 75 Copynumber: 2.9 Consensus size: 76
78767 AAGGTAAAAC
* *
78777 ATCTTAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAACAAAAATAATA
1 ATCTTAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAA-A
*
78841 A-TT-AAAATAAT
64 ATTTAAAAACAAT
78852 ATCTTAAATCCTAATT-AAATACTAAAACCTATTTAAACTAAAATACCTAAAA-AAAGATAAAAT
1 ATCTTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAAT
78915 TTAAAAACAAT
66 TTAAAAACAAT
* * *
78926 ATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAAT
1 ATCTTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAAT
78991 ATAATGTTTA
Statistics
Matches: 128, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
72 2 0.02
73 14 0.11
74 49 0.38
75 52 0.41
76 11 0.09
ACGTcount: A:0.57, C:0.14, G:0.01, T:0.28
Consensus pattern (76 bp):
ATCTTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAAT
TTAAAAACAAT
Found at i:78977 original size:75 final size:75
Alignment explanation
Indices: 78781--78990 Score: 302
Period size: 74 Copynumber: 2.8 Consensus size: 75
78771 TAAAACATCT
* * *
78781 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAACAAAAATAATAA-TT
1 TAAAACCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAA-AATTT
* *
78844 AAAATAATATCT
64 AAAACAATATCC
*
78856 TAAATCCTAATT-AAATACTAAAACCTATTTAAACTAAAATACCTAAAA-AAAGATAAAATTTAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATTT-A
78919 AAACAATATCC
65 AAACAATATCC
*
78930 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAAT
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAAT
78991 ATAATGTTTA
Statistics
Matches: 124, Mismatches: 6, Indels: 9
0.89 0.04 0.06
Matches are distributed among these distances:
72 2 0.02
73 14 0.11
74 49 0.40
75 48 0.39
76 11 0.09
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.28
Consensus pattern (75 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATTTAA
AACAATATCC
Found at i:80446 original size:18 final size:18
Alignment explanation
Indices: 80425--80463 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
80415 ACTTTAGAAA
*
80425 AGAATGTATATTTATATG
1 AGAATGGATATTTATATG
80443 AGAATGGATATTTATATG
1 AGAATGGATATTTATATG
80461 AGA
1 AGA
80464 TGAATGAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (18 bp):
AGAATGGATATTTATATG
Found at i:87352 original size:19 final size:19
Alignment explanation
Indices: 87328--87367 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
87318 TGGAATATTA
87328 TCATTTACCTGTCTACTTC
1 TCATTTACCTGTCTACTTC
87347 TCATTTACCTGTCTACTTC
1 TCATTTACCTGTCTACTTC
87366 TC
1 TC
87368 CAATCTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.05, T:0.47
Consensus pattern (19 bp):
TCATTTACCTGTCTACTTC
Found at i:89645 original size:103 final size:102
Alignment explanation
Indices: 89481--89665 Score: 262
Period size: 103 Copynumber: 1.8 Consensus size: 102
89471 ATACTTCAAA
* * * * * *
89481 GGGAGTCATCTCATCACACTACCATCCCACACTCTAAGTGAAAGGGAGAATACCTTTCACCCTCG
1 GGGAGTCAACCCATAACACTACCATCCCACACTCTAAGTGAAAGAGAGAATACCTTCCACCCCCG
89546 AGCTAGTCAAGTAGAGTTTTTTTAAGCATACATTAAG
66 AGCTAGTCAAGTAGAGTTTTTTTAAGCATACATTAAG
* * *
89583 GGGAGTCAACCCATAACACCTACCATCCCACACTCTAGGTGAAAGAGAGCATGCCTTCCACCCCC
1 GGGAGTCAACCCATAACA-CTACCATCCCACACTCTAAGTGAAAGAGAGAATACCTTCCACCCCC
* *
89648 TAGCTAGTCAGGTAGAGT
65 GAGCTAGTCAAGTAGAGT
89666 CATCCCGTGA
Statistics
Matches: 71, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
102 15 0.21
103 56 0.79
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (102 bp):
GGGAGTCAACCCATAACACTACCATCCCACACTCTAAGTGAAAGAGAGAATACCTTCCACCCCCG
AGCTAGTCAAGTAGAGTTTTTTTAAGCATACATTAAG
Found at i:95255 original size:19 final size:19
Alignment explanation
Indices: 95231--95268 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
95221 TATCACCATA
95231 GGTGGATCGAAATAATTTT
1 GGTGGATCGAAATAATTTT
95250 GGTGGATCGAAATAATTTT
1 GGTGGATCGAAATAATTTT
95269 TTCTCATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (19 bp):
GGTGGATCGAAATAATTTT
Found at i:95946 original size:23 final size:23
Alignment explanation
Indices: 95913--95958 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
95903 TCCTTGAAGG
95913 CATAAAGAATGTGTTCCAAAAGT
1 CATAAAGAATGTGTTCCAAAAGT
* *
95936 CATAAATAATGTGTTCCATAAGT
1 CATAAAGAATGTGTTCCAAAAGT
95959 AATCTGCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.30
Consensus pattern (23 bp):
CATAAAGAATGTGTTCCAAAAGT
Found at i:97972 original size:22 final size:22
Alignment explanation
Indices: 97957--98027 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
97947 ATAATTAGAT
97957 AAATAATACTATATAATAAAATA
1 AAAT-ATACTATATAATAAAATA
*
97980 AAATATA-T-TAT-ATAATATA
1 AAATATACTATATAATAAAATA
* * *
97999 ATATATATTATATAATATAATA
1 AAATATACTATATAATAAAATA
*
98021 TAATATA
1 AAATATA
98028 TGATACCTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
19 13 0.33
20 4 0.10
21 4 0.10
22 14 0.36
23 4 0.10
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATATACTATATAATAAAATA
Found at i:97986 original size:17 final size:17
Alignment explanation
Indices: 97966--98005 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
97956 TAAATAATAC
97966 TATATAATAAAATAAAA
1 TATATAATAAAATAAAA
* * *
97983 TATATTATATAATATAA
1 TATATAATAAAATAAAA
98000 TATATA
1 TATATA
98006 TTATATAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TATATAATAAAATAAAA
Found at i:97998 original size:12 final size:12
Alignment explanation
Indices: 97966--98028 Score: 69
Period size: 12 Copynumber: 5.4 Consensus size: 12
97956 TAAATAATAC
97966 TATATAATA-AA
1 TATATAATATAA
* *
97977 -ATAAAATATAT
1 TATATAATATAA
97988 TATATAATATAA
1 TATATAATATAA
*
98000 TATATATTAT-A
1 TATATAATATAA
98011 TAATATAATATAA
1 T-ATATAATATAA
98024 TATAT
1 TATAT
98029 GATACCTAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
10 7 0.17
11 3 0.07
12 30 0.71
13 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:98019 original size:19 final size:19
Alignment explanation
Indices: 97937--98077 Score: 94
Period size: 19 Copynumber: 7.8 Consensus size: 19
97927 GACCTACAAA
*
97937 ATAA-ATAATA-ATAATTAG
1 ATAATATAATATAT-ATTAT
97955 ATAA-ATAATACTATA-TA-
1 ATAATATAATA-TATATTAT
* *
97972 ATAAAATAAAATATATTAT
1 ATAATATAATATATATTAT
97991 ATAATATAATATATATTAT
1 ATAATATAATATATATTAT
98010 ATAATATAATATA-A-TAT
1 ATAATATAATATATATTAT
*
98027 ATGATACCTAATATA-A-TAGT
1 ATAATA--TAATATATATTA-T
98047 ATAA-A-AATTATATATTA-
1 ATAATATAA-TATATATTAT
98064 AT-ATATAA-ATATAT
1 ATAATATAATATATAT
98078 GTAAAATATA
Statistics
Matches: 105, Mismatches: 5, Indels: 28
0.76 0.04 0.20
Matches are distributed among these distances:
16 9 0.09
17 23 0.22
18 23 0.22
19 44 0.42
20 6 0.06
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
ATAATATAATATATATTAT
Found at i:98024 original size:24 final size:24
Alignment explanation
Indices: 97967--98110 Score: 91
Period size: 24 Copynumber: 6.0 Consensus size: 24
97957 AAATAATACT
* *
97967 ATATAATA-AA-ATAAAATATATT
1 ATATAATATAATATATAATATATA
*
97989 ATATAATATAATATATATTATATA
1 ATATAATATAATATATAATATATA
* **
98013 ATATAATATAATATATGATACCTA
1 ATATAATATAATATATAATATATA
* * *
98037 ATATAATAGTATAAAAATTATATATTA
1 ATATAATA-TA-ATATATAATATA-TA
*
98064 ATAT-ATA-AATATATGTAAAATATA
1 ATATAATATAATATA--TAATATATA
* * *
98088 GTAT-GTAAAATATATAATATATA
1 ATATAATATAATATATAATATATA
98111 TGATACCCAT
Statistics
Matches: 95, Mismatches: 19, Indels: 15
0.74 0.15 0.12
Matches are distributed among these distances:
22 8 0.08
23 13 0.14
24 45 0.47
25 13 0.14
26 10 0.11
27 6 0.06
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (24 bp):
ATATAATATAATATATAATATATA
Found at i:98044 original size:5 final size:5
Alignment explanation
Indices: 97955--98027 Score: 71
Period size: 5 Copynumber: 14.6 Consensus size: 5
97945 TAATAATTAG
* *
97955 ATAA- ATAAT ACT-AT ATAAT AAAAT AAAAT ATATTAT ATAAT ATAAT
1 ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT ATA--AT ATAAT ATAAT
*
98001 AT-AT ATTAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
98028 TGATACCTAA
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
4 9 0.15
5 45 0.75
6 1 0.02
7 5 0.08
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:98092 original size:14 final size:14
Alignment explanation
Indices: 98075--98101 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
98065 TATATAAATA
98075 TATGTAAAATATAG
1 TATGTAAAATATAG
98089 TATGTAAAATATA
1 TATGTAAAATATA
98102 TAATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (14 bp):
TATGTAAAATATAG
Found at i:102786 original size:16 final size:17
Alignment explanation
Indices: 102767--102805 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
102757 GAAAACATGA
102767 AAAAGATAAAA-AAAAT
1 AAAAGATAAAATAAAAT
* *
102783 AAAAGGTAAAATAATAT
1 AAAAGATAAAATAAAAT
102800 AAAAGA
1 AAAAGA
102806 AATATAAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.15
Consensus pattern (17 bp):
AAAAGATAAAATAAAAT
Found at i:102801 original size:26 final size:29
Alignment explanation
Indices: 102772--102825 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
102762 CATGAAAAAG
*
102772 ATAAAA-AAA-ATAAA-AGGTAAAATAAT
1 ATAAAAGAAATATAAACAAGTAAAATAAT
102798 ATAAAAGAAATATAAACAAGTAAAATAA
1 ATAAAAGAAATATAAACAAGTAAAATAA
102826 AAATGCTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 6 0.25
27 3 0.12
28 5 0.21
29 10 0.42
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (29 bp):
ATAAAAGAAATATAAACAAGTAAAATAAT
Found at i:111850 original size:4 final size:4
Alignment explanation
Indices: 111843--111869 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
111833 GAAAGAAAGA
111843 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
111870 AGGGGTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:113282 original size:55 final size:55
Alignment explanation
Indices: 113213--113621 Score: 244
Period size: 55 Copynumber: 7.3 Consensus size: 55
113203 ATAATCCCTA
* * *
113213 AAAGAAAAGGGGAGCAGACATATCTTCCAAAGATTTTTTGAGTCATTTCTCTCTG
1 AAAGAAGAGTGGAGCAGACATGTCTTCCAAAGATTTTTTGAGTCATTTCTCTCTG
** * * * * * *
113268 AAAGAAGAGTGGAGCAGACCCGTCTTATC-AA-TTTTTTTCGAGTCCTATACTCCCTA
1 AAAGAAGAGTGGAGCAGACATGTCTT-CCAAAGATTTTTT-GAGTCAT-TTCTCTCTG
* * *** * *
113324 AAACAAGAGTAGAGCAGACCCATCTTCCGAAGATTTTTCGAGTC-TTATCTCTCTG
1 AAAGAAGAGTGGAGCAGACATGTCTTCCAAAGATTTTTTGAGTCATT-TCTCTCTG
* * * * * * * *
113379 AAAGAATAGTGGA-CTAAACTTGTCTTATCAAA-ATTTTTTCGAGTCCTATACTCCCTA
1 AAAGAAGAGTGGAGC-AGACATGTCTT-CCAAAGATTTTTT-GAGTCAT-TTCTCTCTG
* * *
113436 AAAGAAAAGTGGAGCAGACATGTCTTCCAAAGATTTTTTTAGTC-TTATCTCTCTA
1 AAAGAAGAGTGGAGCAGACATGTCTTCCAAAGATTTTTTGAGTCATT-TCTCTCTG
* *** * * * *
113491 AAAGAAGAGTGGAGCAGGCCCATCTTATCAAATATTTCTCT-AGTCATATACTC-CTTG
1 AAAGAAGAGTGGAGCAGACATGTCTT-CCAAAGATTT-TTTGAGTCAT-TTCTCTC-TG
* * * *
113548 AAAGAATAGTGGAGCAGACATGTTTTCCAAAGATTTTTCGAGTCTAATAT-TC-CTG
1 AAAGAAGAGTGGAGCAGACATGTCTTCCAAAGATTTTTTGAGTC--ATTTCTCTCTG
113603 AAAGAAGAGTGGAGCAGAC
1 AAAGAAGAGTGGAGCAGAC
113622 CCATCTTATC
Statistics
Matches: 269, Mismatches: 63, Indels: 44
0.72 0.17 0.12
Matches are distributed among these distances:
54 9 0.03
55 108 0.40
56 81 0.30
57 66 0.25
58 5 0.02
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (55 bp):
AAAGAAGAGTGGAGCAGACATGTCTTCCAAAGATTTTTTGAGTCATTTCTCTCTG
Found at i:113341 original size:56 final size:57
Alignment explanation
Indices: 113190--113674 Score: 313
Period size: 56 Copynumber: 8.7 Consensus size: 57
113180 AATCCGAAGA
* * * * *** * *
113190 TTTTTT-GAGTTCTATAATCCCTAAAAGAAAAGGGGAGCAGACATATCTT-CCAAAGA
1 TTTTTTCGAGTCCTATACTCCCTAAAAGAAGAGTGGAGCAGACCCGTCTTATCAAA-T
* * * *
113246 TTTTTT-GAGTCAT-TTCTCTCTGAAAGAAGAGTGGAGCAGACCCGTCTTATC-AAT
1 TTTTTTCGAGTCCTATACTCCCTAAAAGAAGAGTGGAGCAGACCCGTCTTATCAAAT
* * * * * *
113300 TTTTTTCGAGTCCTATACTCCCTAAAACAAGAGTAGAGCAGACCCATCTT-CCGAAG
1 TTTTTTCGAGTCCTATACTCCCTAAAAGAAGAGTGGAGCAGACCCGTCTTATCAAAT
* * * * * * ** *
113356 ATTTTTCGAGTCTTAT-CTCTCTGAAAGAATAGTGGA-CTAAACTTGTCTTATCAAAA
1 TTTTTTCGAGTCCTATACTCCCTAAAAGAAGAGTGGAGC-AGACCCGTCTTATCAAAT
* ** *
113412 TTTTTTCGAGTCCTATACTCCCTAAAAGAAAAGTGGAGCAGACATGTCTT-CCAAAGAT
1 TTTTTTCGAGTCCTATACTCCCTAAAAGAAGAGTGGAGCAGACCCGTCTTATC-AA-AT
* * * *
113470 TTTTTT--AGTCTTAT-CTCTCTAAAAGAAGAGTGGAGCAGGCCCATCTTATCAAAT
1 TTTTTTCGAGTCCTATACTCCCTAAAAGAAGAGTGGAGCAGACCCGTCTTATCAAAT
* * * * * * * ** *
113524 ATTTCTCTAGTCATATACTCCTTGAAAGAATAGTGGAGCAGACATGT-TT-TCCAAAG
1 TTTTTTCGAGTCCTATACTCCCTAAAAGAAGAGTGGAGCAGACCCGTCTTAT-CAAAT
* * * *
113580 ATTTTTCGAGT-CTAATA-TTCCTGAAAGAAGAGTGGAGCAGACCCATCTTATC-AAT
1 TTTTTTCGAGTCCT-ATACTCCCTAAAAGAAGAGTGGAGCAGACCCGTCTTATCAAAT
*
113635 TTTTTCTCGAGTCCTATACT-CCTCGAAAGAAGAGTGGAGC
1 TTTTT-TCGAGTCCTATACTCCCT-AAAAGAAGAGTGGAGC
113675 GGTTTCTGTT
Statistics
Matches: 331, Mismatches: 76, Indels: 43
0.74 0.17 0.10
Matches are distributed among these distances:
54 13 0.04
55 117 0.35
56 123 0.37
57 70 0.21
58 8 0.02
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (57 bp):
TTTTTTCGAGTCCTATACTCCCTAAAAGAAGAGTGGAGCAGACCCGTCTTATCAAAT
Found at i:113472 original size:112 final size:111
Alignment explanation
Indices: 113189--113674 Score: 561
Period size: 112 Copynumber: 4.4 Consensus size: 111
113179 AAATCCGAAG
* * * *
113189 ATTTTTT-GAGTTCTATAATCCCTAAAAGAAAAGGGGAGCAGACATATCTTCCAAAGATTTTTTG
1 ATTTTTTCGAGTCCTATACTCCCTAAAAGAAAAGTGGAGCAGACATATCTTCCAAAGATTTTTCG
*
113253 AGTCATT-TCTCTCTGAAAGAAGAGTGGAGCAGACCCGTCTTATCAA
66 AGTC-TTATCTCTCTGAAAGAAGAGTGGAGCAGACCCATCTTATCAA
* * * * ** *
113299 TTTTTTTCGAGTCCTATACTCCCTAAAACAAGAGTAGAGCAGACCCATCTTCCGAAGATTTTTCG
1 ATTTTTTCGAGTCCTATACTCCCTAAAAGAAAAGTGGAGCAGACATATCTTCCAAAGATTTTTCG
* * ***
113364 AGTCTTATCTCTCTGAAAGAATAGTGGA-CTAAACTTGTCTTATCAAA
66 AGTCTTATCTCTCTGAAAGAAGAGTGGAGC-AGACCCATCTTATC-AA
* **
113411 ATTTTTTCGAGTCCTATACTCCCTAAAAGAAAAGTGGAGCAGACATGTCTTCCAAAGATTTTTTT
1 ATTTTTTCGAGTCCTATACTCCCTAAAAGAAAAGTGGAGCAGACATATCTTCCAAAGATTTTTCG
* *
113476 AGTCTTATCTCTCTAAAAGAAGAGTGGAGCAGGCCCATCTTATCAA
66 AGTCTTATCTCTCTGAAAGAAGAGTGGAGCAGACCCATCTTATCAA
* * * * * * * *
113522 ATATTTCTCTAGTCATATACTCCTTGAAAGAATAGTGGAGCAGACATGTTTTCCAAAGATTTTTC
1 AT-TTTTTCGAGTCCTATACTCCCTAAAAGAAAAGTGGAGCAGACATATCTTCCAAAGATTTTTC
113587 GAGTCTAATAT-TC-CTGAAAGAAGAGTGGAGCAGACCCATCTTATCAA
65 GAGTCT--TATCTCTCTGAAAGAAGAGTGGAGCAGACCCATCTTATCAA
* * *
113634 TTTTTTCTCGAGTCCTATACT-CCTCGAAAGAAGAGTGGAGC
1 ATTTTT-TCGAGTCCTATACTCCCT-AAAAGAAAAGTGGAGC
113675 GGTTTCTGTT
Statistics
Matches: 317, Mismatches: 49, Indels: 18
0.83 0.13 0.05
Matches are distributed among these distances:
110 9 0.03
111 91 0.29
112 211 0.67
113 3 0.01
114 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (111 bp):
ATTTTTTCGAGTCCTATACTCCCTAAAAGAAAAGTGGAGCAGACATATCTTCCAAAGATTTTTCG
AGTCTTATCTCTCTGAAAGAAGAGTGGAGCAGACCCATCTTATCAA
Found at i:115161 original size:16 final size:16
Alignment explanation
Indices: 115140--115170 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
115130 CAATCAATCA
115140 ATCCACAAATTCAAAC
1 ATCCACAAATTCAAAC
115156 ATCCACAAATTCAAA
1 ATCCACAAATTCAAA
115171 TATTCAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (16 bp):
ATCCACAAATTCAAAC
Found at i:127162 original size:39 final size:39
Alignment explanation
Indices: 127073--127194 Score: 113
Period size: 39 Copynumber: 3.1 Consensus size: 39
127063 TAAGGTTTTC
* * * *
127073 CCCTATGCACGAAGCAAATGAGATTA-CAGTAAGTACTTA
1 CCCTATGCACAAAGCAAAGGAG-TTAGCGGTAAGGACTTA
* *
127112 CTCTGTGCACAAAGCAAAGGAGTTAGCGGTAAGGACTTA
1 CCCTATGCACAAAGCAAAGGAGTTAGCGGTAAGGACTTA
* * * * *
127151 CCCTATACACAAAACAAAGGAG-CATGTGGTAATGACTTA
1 CCCTATGCACAAAGCAAAGGAGTTA-GCGGTAAGGACTTA
127190 CCCTA
1 CCCTA
127195 GCCGTAGCGT
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
38 4 0.06
39 64 0.94
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.21
Consensus pattern (39 bp):
CCCTATGCACAAAGCAAAGGAGTTAGCGGTAAGGACTTA
Found at i:128298 original size:27 final size:27
Alignment explanation
Indices: 128228--128298 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
128218 TCAAAGCTCG
* *
128228 GGGTATTTTGGTCATTTTAAAGTTTAA
1 GGGTATTTTAGTCATTTTAAAGTTCAA
* *
128255 GGGTATTTTAGTAATTTTAGAGTTCAA
1 GGGTATTTTAGTCATTTTAAAGTTCAA
*
128282 GGGTATTTTATTCATTT
1 GGGTATTTTAGTCATTT
128299 CATTCAATCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.25, C:0.04, G:0.21, T:0.49
Consensus pattern (27 bp):
GGGTATTTTAGTCATTTTAAAGTTCAA
Found at i:136334 original size:9 final size:9
Alignment explanation
Indices: 136320--136369 Score: 64
Period size: 9 Copynumber: 5.3 Consensus size: 9
136310 CGCTGGAAAA
136320 ACCGGTTTG
1 ACCGGTTTG
136329 ACCGGTTTTG
1 ACCGG-TTTG
*
136339 ATCGGTTTG
1 ACCGGTTTG
*
136348 ACCAGTTTTG
1 ACC-GGTTTG
136358 ACCGGTTTG
1 ACCGGTTTG
136367 ACC
1 ACC
136370 CGACCGACCG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
9 19 0.54
10 16 0.46
ACGTcount: A:0.14, C:0.22, G:0.28, T:0.36
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:136346 original size:19 final size:19
Alignment explanation
Indices: 136320--136369 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
136310 CGCTGGAAAA
*
136320 ACCGGTTTGACCGGTTTTG
1 ACCGGTTTGACCAGTTTTG
*
136339 ATCGGTTTGACCAGTTTTG
1 ACCGGTTTGACCAGTTTTG
136358 ACCGGTTTGACC
1 ACCGGTTTGACC
136370 CGACCGACCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.14, C:0.22, G:0.28, T:0.36
Consensus pattern (19 bp):
ACCGGTTTGACCAGTTTTG
Found at i:143616 original size:9 final size:9
Alignment explanation
Indices: 143602--143636 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
143592 CGCTGGAAAA
143602 ACCGGTTTG
1 ACCGGTTTG
*
143611 ACCGGTTCTA
1 ACCGGTT-TG
143621 ACCGGTTTG
1 ACCGGTTTG
143630 ACCGGTT
1 ACCGGTT
143637 CAACCCAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.14, C:0.26, G:0.29, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:143625 original size:19 final size:18
Alignment explanation
Indices: 143601--143641 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 18
143591 ACGCTGGAAA
143601 AACCGGTTTGACCGGTTC
1 AACCGGTTTGACCGGTTC
143619 TAACCGGTTTGACCGGTTC
1 -AACCGGTTTGACCGGTTC
143638 AACC
1 AACC
143642 CAACCGACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (18 bp):
AACCGGTTTGACCGGTTC
Found at i:143678 original size:13 final size:13
Alignment explanation
Indices: 143660--143693 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
143650 CCGACCCGAT
143660 CGTTGACCGTGAC
1 CGTTGACCGTGAC
*
143673 CGTTGACTGTGAC
1 CGTTGACCGTGAC
143686 CGTTGACC
1 CGTTGACC
143694 CCCTTTGACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.26
Consensus pattern (13 bp):
CGTTGACCGTGAC
Found at i:147555 original size:10 final size:10
Alignment explanation
Indices: 147535--147574 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
147525 TTGGACCGAA
147535 AAATAAAAAAT
1 AAAT-AAAAAT
147546 AAATAAAAAT
1 AAATAAAAAT
147556 AAAT-AAAAT
1 AAATAAAAAT
147565 AAAATAAAAA
1 -AAATAAAAA
147575 CAGAAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 5 0.19
10 14 0.52
11 8 0.30
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:147643 original size:17 final size:18
Alignment explanation
Indices: 147621--147654 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
147611 CTTTCGAAAA
147621 ATATGTTTT-CAAAAACT
1 ATATGTTTTCCAAAAACT
147638 ATATGTTTTCCAAAAAC
1 ATATGTTTTCCAAAAAC
147655 CATTTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (18 bp):
ATATGTTTTCCAAAAACT
Found at i:147676 original size:37 final size:36
Alignment explanation
Indices: 147635--147910 Score: 161
Period size: 37 Copynumber: 7.5 Consensus size: 36
147625 GTTTTCAAAA
147635 ACTATATGTTTTCCAAAAACCATTTT-AAAAACTATAT
1 ACTATATGTTTT-CAAAAA-CATTTTAAAAAACTATAT
* *
147672 ACTATATGTTTTCAAAAATATCTTTAAAAAAATTATAT
1 ACTATATGTTTTCAAAAACAT-TTT-AAAAAACTATAT
* *
147710 AATATATG-TTTCAAAAATACATTTTCAAAAACTATATT
1 ACTATATGTTTTC-AAAA-ACATTTTAAAAAACTATA-T
* *
147748 A-TATATTGTTTTCAAAAATA-TTT-AAAAACTAAAT
1 ACTATA-TGTTTTCAAAAACATTTTAAAAAACTATAT
* * ** ***
147782 ATTATACGTTTTCAAAAATGTGTTTTCGAAACTATAT
1 ACTATATGTTTTCAAAAACAT-TTTAAAAAACTATAT
** * * ** ** *
147819 GTTATACGTTTTTAAAAATGTGTTTTCAAAACCATAT
1 ACTATATGTTTTCAAAAACAT-TTTAAAAAACTATAT
** *
147856 --TATATGTTTTACAAAATTGATTTTTAAAAACTATAT
1 ACTATATGTTTT-CAAAA-ACATTTTAAAAAACTATAT
*
147892 ATTATATGTTTTCAAAAAC
1 ACTATATGTTTTCAAAAAC
147911 TATACTATAT
Statistics
Matches: 197, Mismatches: 26, Indels: 33
0.77 0.10 0.13
Matches are distributed among these distances:
34 14 0.07
35 24 0.12
36 32 0.16
37 78 0.40
38 42 0.21
39 7 0.04
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (36 bp):
ACTATATGTTTTCAAAAACATTTTAAAAAACTATAT
Found at i:147717 original size:75 final size:74
Alignment explanation
Indices: 147637--147775 Score: 196
Period size: 75 Copynumber: 1.9 Consensus size: 74
147627 TTTCAAAAAC
*
147637 TATATGTTTTCCAAAAA-CCATTTT-AAAAACTATA-TACTATA-TGTTTTCAAAAATATCTTTA
1 TATATG-TTT-CAAAAATACATTTTCAAAAACTATATTA-TATATTGTTTTCAAAAATA--TTTA
147698 AAAAAATTATATAA
61 AAAAAATTATATAA
147712 TATATGTTTCAAAAATACATTTTCAAAAACTATATTATATATTGTTTTCAAAAATATTTAAAAA
1 TATATGTTTCAAAAATACATTTTCAAAAACTATATTATATATTGTTTTCAAAAATATTTAAAAA
147776 CTAAATATTA
Statistics
Matches: 59, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
73 6 0.10
74 17 0.29
75 20 0.34
76 16 0.27
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (74 bp):
TATATGTTTCAAAAATACATTTTCAAAAACTATATTATATATTGTTTTCAAAAATATTTAAAAAA
ATTATATAA
Found at i:147808 original size:73 final size:70
Alignment explanation
Indices: 147637--147909 Score: 198
Period size: 72 Copynumber: 3.7 Consensus size: 70
147627 TTTCAAAAAC
***
147637 TATATGTTTTCCAAAAACCATTTT-AAAAACTATATACTATATGTTTTCAAAAATATCTTTAAAA
1 TATATGTTTT-CAAAAATTGTTTTCAAAAACTATATA-TATATGTTTTCAAAAATA--TTT--AA
* * *
147701 AAATTATATAA
60 AAACTAAATAT
**
147712 TATATG-TTTCAAAAATACATTTTCAAAAACTATATTATATATTGTTTTCAAAAATATTTAAAAA
1 TATATGTTTTCAAAAAT-TGTTTTCAAAAACTATA-TATATA-TGTTTTCAAAAATATTTAAAAA
147776 CTAAATAT
63 CTAAATAT
* * * * * * *
147784 TATACGTTTTCAAAAATGTGTTTTC-GAAACTATATGTTATACGTTTTTAAAAATGTGTTTTCAA
1 TATATGTTTTCAAAAAT-TGTTTTCAAAAACTATAT-ATATATGTTTTCAAAAA--T-ATTTAAA
*
147848 AAC--CATAT
61 AACTAAATAT
*
147856 TATATGTTTT-ACAAAATTGATTTTTAAAAACTATATATTATATGTTTTCAAAAA
1 TATATGTTTTCA-AAAATTG-TTTTCAAAAACTATATA-TATATGTTTTCAAAAA
147910 CTATACTATA
Statistics
Matches: 164, Mismatches: 21, Indels: 28
0.77 0.10 0.13
Matches are distributed among these distances:
71 14 0.09
72 49 0.30
73 45 0.27
74 20 0.12
75 20 0.12
76 16 0.10
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.42
Consensus pattern (70 bp):
TATATGTTTTCAAAAATTGTTTTCAAAAACTATATATATATGTTTTCAAAAATATTTAAAAACTA
AATAT
Found at i:148521 original size:22 final size:22
Alignment explanation
Indices: 148492--148543 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
148482 TTGTTCATTA
*
148492 CTACAGTAACTGTTACAGTAAG
1 CTACAGTAACTGCTACAGTAAG
* * *
148514 CTATAGTAGCTGCTACATTAAG
1 CTACAGTAACTGCTACAGTAAG
148536 CTACAGTA
1 CTACAGTA
148544 CTTCTGAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (22 bp):
CTACAGTAACTGCTACAGTAAG
Found at i:149050 original size:45 final size:45
Alignment explanation
Indices: 148931--149290 Score: 519
Period size: 45 Copynumber: 8.0 Consensus size: 45
148921 TACAACTTTC
* * *
148931 TTACCAATATACATATCATTTAT-CCTATAAGCTCGTAAGCTTATT
1 TTACCCATATACTTACCATTTATACC-ATAAGCTCGTAAGCTTATT
* * * *
148976 TTA-CTACATACTTACCATTTATTCCATAAGCTCATAAGCTTATT
1 TTACCCATATACTTACCATTTATACCATAAGCTCGTAAGCTTATT
* *** *
149020 TTACCAATATACTTACCATTTATTTTATAAGCTAGTAAGCTTATT
1 TTACCCATATACTTACCATTTATACCATAAGCTCGTAAGCTTATT
*
149065 TTATCCATATACTTACCATTTATACCATAAGCTCGTAAGCTTATT
1 TTACCCATATACTTACCATTTATACCATAAGCTCGTAAGCTTATT
149110 TTACCCATATACTTACCATTTATACCATAAGCTCGTAAGCTTATT
1 TTACCCATATACTTACCATTTATACCATAAGCTCGTAAGCTTATT
* *
149155 TTACCCATATACTTATCATTTATACCATAAGCTTGTAAGCTTATT
1 TTACCCATATACTTACCATTTATACCATAAGCTCGTAAGCTTATT
*
149200 TTACCCATATACTTACTATTTATACCATAAGCTCGTAAGCTTATT
1 TTACCCATATACTTACCATTTATACCATAAGCTCGTAAGCTTATT
* * *
149245 TTACCCATATACTTGCCA-TCATTCCATAAGCTCGTAAGCTTATT
1 TTACCCATATACTTACCATTTATACCATAAGCTCGTAAGCTTATT
149289 TT
1 TT
149291 CATGCTTACC
Statistics
Matches: 286, Mismatches: 27, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
44 62 0.22
45 224 0.78
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.41
Consensus pattern (45 bp):
TTACCCATATACTTACCATTTATACCATAAGCTCGTAAGCTTATT
Found at i:149092 original size:20 final size:20
Alignment explanation
Indices: 149064--149138 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 20
149054 GTAAGCTTAT
149064 TTTAT-CCATATACTTACCA
1 TTTATACCATATACTTACCA
*
149083 TTTATACCATA-AGCTCGTAAGCTTA
1 TTTATACCATATA-CT--T-A-C-CA
149108 TTT-TACCCATATACTTACCA
1 TTTATA-CCATATACTTACCA
149128 TTTATACCATA
1 TTTATACCATA
149139 AGCTCGTAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 19
0.68 0.03 0.29
Matches are distributed among these distances:
19 6 0.14
20 16 0.36
21 3 0.07
22 2 0.05
23 2 0.05
24 3 0.07
25 11 0.25
26 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (20 bp):
TTTATACCATATACTTACCA
Found at i:149505 original size:61 final size:61
Alignment explanation
Indices: 149398--149512 Score: 187
Period size: 61 Copynumber: 1.9 Consensus size: 61
149388 GTAGTGCTAA
*
149398 ACCTGCACTAAGCTTAAGCTATAGTGCTAATCCGGACAATACACATAAGGTCGTGCCCACC
1 ACCTACACTAAGCTTAAGCTATAGTGCTAATCCGGACAATACACATAAGGTCGTGCCCACC
* *
149459 ACCTACACTAAGCTTACGCTATAGTGCTAATCCGGAC-ATGATACATAAGGTCGT
1 ACCTACACTAAGCTTAAGCTATAGTGCTAATCCGGACAAT-ACACATAAGGTCGT
149513 ATCCACCTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
60 2 0.04
61 48 0.96
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.23
Consensus pattern (61 bp):
ACCTACACTAAGCTTAAGCTATAGTGCTAATCCGGACAATACACATAAGGTCGTGCCCACC
Found at i:153134 original size:14 final size:14
Alignment explanation
Indices: 153101--153142 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
153091 AGTGAATTTT
*
153101 TTTTTCATCTTTCATT
1 TTTTTC-TCTTTC-TC
153117 TTTTTCTCTTTCTC
1 TTTTTCTCTTTCTC
153131 TTTTTCT-TTTCT
1 TTTTTCTCTTTCT
153143 TTTCTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 6 0.24
16 6 0.24
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTCTCTTTCTC
Found at i:153135 original size:17 final size:16
Alignment explanation
Indices: 153098--153204 Score: 62
Period size: 16 Copynumber: 6.3 Consensus size: 16
153088 ACCAGTGAAT
153098 TTTTTTTTCATC-TTTC
1 TTTTTTTTC-TCTTTTC
*
153114 ATTTTTTTCTCTTTCTC
1 TTTTTTTTCTCTTT-TC
153131 TTTTTCTTT-TCTTTTC
1 TTTTT-TTTCTCTTTTC
153147 TTTTTCTATT-T-TTTTC
1 TTTTT-T-TTCTCTTTTC
*
153163 ATTTTCATTTTCATTTTATTC
1 -TTTT--TTTTC-TCTT-TTC
153184 TTTCTTTTT-TCTTTTC
1 TTT-TTTTTCTCTTTTC
153200 TTTTT
1 TTTTT
153205 ATACTATATA
Statistics
Matches: 76, Mismatches: 3, Indels: 25
0.73 0.03 0.24
Matches are distributed among these distances:
15 4 0.05
16 30 0.39
17 23 0.30
18 4 0.05
19 6 0.08
20 5 0.07
21 4 0.05
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTTTCTCTTTTC
Found at i:153191 original size:12 final size:12
Alignment explanation
Indices: 153116--153204 Score: 71
Period size: 12 Copynumber: 7.4 Consensus size: 12
153106 CATCTTTCAT
153116 TTTTTTCTCTTTC
1 TTTTTTCT-TTTC
153129 TCTTTTTCTTTTC
1 T-TTTTTCTTTTC
*
153142 TTTTCT-TTTTC
1 TTTTTTCTTTTC
*
153153 -TATTT-TTTTC
1 TTTTTTCTTTTC
*
153163 -ATTTTCATTTTC
1 TTTTTTC-TTTTC
153175 ATTTTATTC-TTTC
1 -TTTT-TTCTTTTC
153188 TTTTTTCTTTTC
1 TTTTTTCTTTTC
153200 TTTTT
1 TTTTT
153205 ATACTATATA
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
10 11 0.17
11 8 0.13
12 22 0.35
13 10 0.16
14 9 0.14
15 3 0.05
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTCTTTTC
Found at i:153204 original size:6 final size:6
Alignment explanation
Indices: 153117--153204 Score: 60
Period size: 6 Copynumber: 14.8 Consensus size: 6
153107 ATCTTTCATT
*
153117 TTTTTC TCTTTCTC TTTTTC -TTTTC -TTTTC TTTTTC -TATT- TTTTTC
1 TTTTTC T-TTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* * * *
153163 ATTTTC ATTTTC ATTTTA TTCTTTC TTTTT- TCTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TT-TTTC TTTTTC T-TTTTC TTTTT
153205 ATACTATATA
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
5 17 0.25
6 36 0.53
7 12 0.18
8 3 0.04
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:156224 original size:9 final size:9
Alignment explanation
Indices: 156197--156253 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
156187 TTTGGACCTG
*
156197 AAAATAAAA
1 AAAATAAAT
156206 AAAATGAAAT
1 AAAAT-AAAT
156216 AAAATAAAT
1 AAAATAAAT
*
156225 AATATAAAT
1 AAAATAAAT
*
156234 -AACTAAAT
1 AAAATAAAT
*
156242 ATAAT-AAT
1 AAAATAAAT
156250 AAAA
1 AAAA
156254 ACTATATAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
8 12 0.31
9 19 0.49
10 8 0.21
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (9 bp):
AAAATAAAT
Found at i:156247 original size:19 final size:16
Alignment explanation
Indices: 156223--156265 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 16
156213 AATAAAATAA
156223 ATAATATAAATAACTAAAT
1 ATAATATAAA-AACT--AT
156242 ATAATAATAAAAACTAT
1 ATAAT-ATAAAAACTAT
156259 ATAATAT
1 ATAATAT
156266 TATATTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.09
17 7 0.30
19 9 0.39
20 5 0.22
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAATATAAAAACTAT
Found at i:156324 original size:23 final size:22
Alignment explanation
Indices: 156279--156322 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
156269 ATTTTCATAA
*
156279 ATATGTTTTCAAAAATTATTTT
1 ATATGTTTTCAAAAATCATTTT
156301 ATATGTTTTCAAAAATCATTTT
1 ATATGTTTTCAAAAATCATTTT
156323 TAAAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (22 bp):
ATATGTTTTCAAAAATCATTTT
Found at i:156359 original size:35 final size:35
Alignment explanation
Indices: 156249--156709 Score: 392
Period size: 36 Copynumber: 12.8 Consensus size: 35
156239 AATATAATAA
* * *
156249 TAAAAACTATATAATATTATATTTTCATAAATATGTTT
1 TAAAAACTATATATTA-TATGTTTTCA-AAAT-TATTT
* *
156287 TCAAAAA-T-TATTTTATATGTTTTCAAAAATCATTTT
1 T-AAAAACTATATATTATATGTTTTC-AAAATTA-TTT
*
156323 TAAAAAATATATATTATATGTTTTCAAAATTATTT
1 TAAAAACTATATATTATATGTTTTCAAAATTATTT
** * **
156358 TAAAAACTATATACCATATGTTTTTAAAAATCGTTT
1 TAAAAACTATATATTATATG-TTTTCAAAATTATTT
**
156394 TAAAAACTATATATTATACATTTTCAAAATTATTT
1 TAAAAACTATATATTATATGTTTTCAAAATTATTT
*
156429 TAAAAAC--TATATTATAAGTTTTCAAAATTATTT
1 TAAAAACTATATATTATATGTTTTCAAAATTATTT
* * ***
156462 AAAAAACTATATACTATATGTTTTCAAAACCGTTT
1 TAAAAACTATATATTATATGTTTTCAAAATTATTT
* * *
156497 TAAAAACTATATATTATACGTTTTTAAAACTATTTTT
1 TAAAAACTATATATTATATGTTTTCAAAA-T-TATTT
* * ** *
156534 TAAAAGCTATATATTATACGTTTTCAATTTTTTTT
1 TAAAAACTATATATTATATGTTTTCAAAATTATTT
*
156569 TAAAAAGCTATATATTATACGTTTTCAAAATTATTT
1 TAAAAA-CTATATATTATATGTTTTCAAAATTATTT
* * * * ***
156605 TGAAAACTTTTTTACTATATGTTTTCAAAACCGTTT
1 TAAAAAC-TATATATTATATGTTTTCAAAATTATTT
* *
156641 TAAAAACTATATATTATATGTTTTTAAAAAATAAGTTT
1 TAAAAACTATATATTATATG-TTTT-CAAAATTA-TTT
*
156679 CCAAAAACTATATATTACATAT-TTTTCAAAA
1 -TAAAAACTATATATT--ATATGTTTTCAAAA
156710 ACTATATTTG
Statistics
Matches: 344, Mismatches: 61, Indels: 36
0.78 0.14 0.08
Matches are distributed among these distances:
33 30 0.09
35 111 0.32
36 114 0.33
37 53 0.15
38 9 0.03
39 23 0.07
41 4 0.01
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.46
Consensus pattern (35 bp):
TAAAAACTATATATTATATGTTTTCAAAATTATTT
Found at i:156455 original size:104 final size:106
Alignment explanation
Indices: 156306--156582 Score: 346
Period size: 104 Copynumber: 2.6 Consensus size: 106
156296 ATTTTATATG
* * *
156306 TTTTCAAAAATCAT-TTTTAAAAAATATATATTATATGTTTTCAAAATTATTTTAAAAACTATAT
1 TTTTCAAAACT-ATATTTT-AAAAACATATATTATAAGTTTTCAAAATTATTTTAAAAACTATAT
*
156370 ACCATATGTTTTTAAAAATCGTTTTAAAAACTATATATTATACA
64 ACCATATG-TTTTAAAAACCGTTTTAAAAACTATATATTATACA
*
156414 TTTTCAAAA-T-TATTTTAAAAAC-TATATTATAAGTTTTCAAAATTATTTAAAAAACTATATAC
1 TTTTCAAAACTATATTTTAAAAACATATATTATAAGTTTTCAAAATTATTTTAAAAACTATATAC
* * *
156476 TATATGTTTTCAAAACCGTTTTAAAAACTATATATTATACG
66 CATATGTTTTAAAAACCGTTTTAAAAACTATATATTATACA
* * * * ** *
156517 TTTTTAAAACTATTTTTTAAAAGCTATATATTATACGTTTTCAATTTTTTTTTAAAAAGCTATAT
1 TTTTCAAAACTATATTTTAAAAAC-ATATATTATAAGTTTTCAAAATTATTTTAAAAA-CTATAT
156582 A
64 A
156583 TTATACGTTT
Statistics
Matches: 148, Mismatches: 15, Indels: 12
0.85 0.09 0.07
Matches are distributed among these distances:
103 40 0.27
104 44 0.30
105 16 0.11
106 4 0.03
107 28 0.19
108 16 0.11
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (106 bp):
TTTTCAAAACTATATTTTAAAAACATATATTATAAGTTTTCAAAATTATTTTAAAAACTATATAC
CATATGTTTTAAAAACCGTTTTAAAAACTATATATTATACA
Found at i:158262 original size:33 final size:33
Alignment explanation
Indices: 158224--158290 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
158214 CCTAGTACAG
158224 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
*
158257 ATGGTGGACACGACCTTATGTGTTATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
158290 A
1 A
158291 ACACTACGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (33 bp):
ATGGTGGACACGACCTTATGTGTCATACGGATT
Found at i:158496 original size:46 final size:45
Alignment explanation
Indices: 158390--158554 Score: 201
Period size: 45 Copynumber: 3.7 Consensus size: 45
158380 ATAACCAGGC
* ** *
158390 AAATAAGCTTACGAGCTTATGGAAT-AATGACAAATATATTGATA
1 AAATAAGCTTACGAGCTTAGGGAATAAATGGTAAGTATATTGATA
* *
158434 AAATAAGCTTACGAGCTTAGGGAATTAAATGGTAAGTATAATGGTA
1 AAATAAGCTTACGAGCTTAGGGAA-TAAATGGTAAGTATATTGATA
* *
158480 AAATAAGCTTACGAGCTTATTGG-ATAAAGGGTAAGTATATTGATA
1 AAATAAGCTTACGAGCTTA-GGGAATAAATGGTAAGTATATTGATA
*
158525 AAATAAGATTACGAGCTTAAGGG-ATAAATG
1 AAATAAGCTTACGAGCTT-AGGGAATAAATG
158555 ATATGTATGT
Statistics
Matches: 104, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
44 23 0.22
45 44 0.42
46 35 0.34
47 2 0.02
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.28
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTAGGGAATAAATGGTAAGTATATTGATA
Found at i:158570 original size:90 final size:90
Alignment explanation
Indices: 158390--158562 Score: 235
Period size: 91 Copynumber: 1.9 Consensus size: 90
158380 ATAACCAGGC
* *
158390 AAATAAGCTTACGAGCTTATGGAATAATGACAAATATATTGATAAAATAAGCTTACGAGCTTAGG
1 AAATAAGCTTACGAGCTTATGGAATAAGGACAAATATATTGATAAAATAAGATTACGAGCTTAGG
*
158455 GAATTAAATGGTAAGTATAATGGTA
66 GAATTAAATGATAAGTATAATGGTA
** *
158480 AAATAAGCTTACGAGCTTATTGG-ATAAAGGGTAAGTATATTGATAAAATAAGATTACGAGCTTA
1 AAATAAGCTTACGAGCTTA-TGGAAT-AAGGACAAATATATTGATAAAATAAGATTACGAGCTT-
*
158544 AGGG-A-TAAATGATATGTAT
63 AGGGAATTAAATGATAAGTAT
158563 GTTGGTAAGA
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
90 33 0.45
91 36 0.49
92 4 0.05
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (90 bp):
AAATAAGCTTACGAGCTTATGGAATAAGGACAAATATATTGATAAAATAAGATTACGAGCTTAGG
GAATTAAATGATAAGTATAATGGTA
Found at i:159026 original size:13 final size:13
Alignment explanation
Indices: 158996--159045 Score: 82
Period size: 13 Copynumber: 3.7 Consensus size: 13
158986 CGATTCCCCC
158996 ACTGTTCACGAGGGT
1 ACTGTTCAC-A-GGT
159011 ACTGTTCACAGGT
1 ACTGTTCACAGGT
159024 ACTGTTCACAGGT
1 ACTGTTCACAGGT
159037 ACTGTTCAC
1 ACTGTTCAC
159046 TATTTAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 25 0.71
14 1 0.03
15 9 0.26
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (13 bp):
ACTGTTCACAGGT
Found at i:161309 original size:40 final size:40
Alignment explanation
Indices: 161265--161343 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
161255 TGGGAAGTTC
* * **
161265 ATGAACAAGGTTTTATGTTTGTTTAATTAAATAAATGAAT
1 ATGAACAAAGTTTTATGCTCATTTAATTAAATAAATGAAT
*
161305 ATGAACAAAGTTTTATGCTCATTTAATTAAATGAATGAA
1 ATGAACAAAGTTTTATGCTCATTTAATTAAATAAATGAA
161344 CACAAACAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (40 bp):
ATGAACAAAGTTTTATGCTCATTTAATTAAATAAATGAAT
Found at i:161352 original size:40 final size:40
Alignment explanation
Indices: 161268--161352 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
161258 GAAGTTCATG
* * ** * **
161268 AACAAGGTTTTATGTTTGTTTAATTAAATAAATGAATATG
1 AACAAAGTTTTATGCTCATTTAATTAAATAAATGAACACA
*
161308 AACAAAGTTTTATGCTCATTTAATTAAATGAATGAACACA
1 AACAAAGTTTTATGCTCATTTAATTAAATAAATGAACACA
161348 AACAA
1 AACAA
161353 TTGACTCATT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (40 bp):
AACAAAGTTTTATGCTCATTTAATTAAATAAATGAACACA
Found at i:161431 original size:32 final size:32
Alignment explanation
Indices: 161385--161451 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
161375 TTCATGAACG
* *
161385 TTTGATAATTCGTTCATTTATGTT-CATTTATA
1 TTTGATAATCCGTTCATTTA-GTTAAATTTATA
* *
161417 TTTGGTAATCCGTTCGTTTAGTTAAATTTATA
1 TTTGATAATCCGTTCATTTAGTTAAATTTATA
161449 TTT
1 TTT
161452 ATCTTTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 3 0.10
32 27 0.90
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (32 bp):
TTTGATAATCCGTTCATTTAGTTAAATTTATA
Found at i:164503 original size:45 final size:46
Alignment explanation
Indices: 164439--164534 Score: 126
Period size: 45 Copynumber: 2.1 Consensus size: 46
164429 CATCGTTTGT
*
164439 ATTTTCATTTGAGGTATCCTTTCATG-CCAATAATGCACTGTT-TAC
1 ATTTTCATTTGAGGTATCCTTTCA-GACCAATAATGCACTATTGTAC
* *
164484 ATTTTCATTT-ATGGTATCCTTTCAGACCAATTATGCATTATTGTAC
1 ATTTTCATTTGA-GGTATCCTTTCAGACCAATAATGCACTATTGTAC
164530 ATTTT
1 ATTTT
164535 ATATATAGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
44 2 0.04
45 35 0.78
46 8 0.18
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.46
Consensus pattern (46 bp):
ATTTTCATTTGAGGTATCCTTTCAGACCAATAATGCACTATTGTAC
Found at i:164995 original size:42 final size:43
Alignment explanation
Indices: 164948--165041 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 43
164938 AGGCTCAATA
* * * * *
164948 GTATCGATACCCTTAC-CATGGTATTGATACTTCTATATTATG
1 GTATCGATACCCTTACTCATAGTATCGATACTACTACACTATG
* *
164990 GTATCGATA-CCTTTCTCTTAGTATCGATACTACTACACTATG
1 GTATCGATACCCTTACTCATAGTATCGATACTACTACACTATG
165032 GTATCGATAC
1 GTATCGATAC
165042 TCCCTTTCAG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 5 0.12
42 38 0.88
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (43 bp):
GTATCGATACCCTTACTCATAGTATCGATACTACTACACTATG
Found at i:173318 original size:25 final size:25
Alignment explanation
Indices: 173282--173332 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
173272 GTATAATACT
173282 AAAACTATTACTTTAATTAC-ATTAC
1 AAAACTATTAC-TTAATTACAATTAC
*
173307 AAAA-TATATACTTAATTTCAATTAC
1 AAAACTAT-TACTTAATTACAATTAC
173332 A
1 A
173333 TGCCAGCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (25 bp):
AAAACTATTACTTAATTACAATTAC
Found at i:173937 original size:2 final size:2
Alignment explanation
Indices: 173930--173958 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
173920 TGTTGTACAT
173930 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
173959 CATCCTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:174234 original size:81 final size:81
Alignment explanation
Indices: 174058--174266 Score: 283
Period size: 81 Copynumber: 2.6 Consensus size: 81
174048 AACTTGTATG
* * *
174058 ATTGACACATTTCTGCCAAATGCAAAACTAGACTATTAATCTTTTACTCAAAGGTATTTAACCTT
1 ATTGACACACTTCTGTCAAATGCACAACTAGACTATTAATCTTTTACTCAAAGGTATTTAACCTT
174123 TCATCTAACAGGCATA
66 TCATCTAACAGGCATA
* * * *
174139 ATTGACATATTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTACTCAAAGGTATTTAAGCTT
1 ATTGACACACTTCTGTCAAATGCACAACTAGACTATTAATCTTTTACTCAAAGGTATTTAACCTT
*
174204 TCATCTAACTGGCATA
66 TCATCTAACAGGCATA
* * * * * * *
174220 ATTGGCACCCTTCTGTGAAATGGACATCTAGCCTATTAATATTTTAC
1 ATTGACACACTTCTGTCAAATGCACAACTAGACTATTAATCTTTTAC
174267 ATGAAACAAT
Statistics
Matches: 113, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 113 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (81 bp):
ATTGACACACTTCTGTCAAATGCACAACTAGACTATTAATCTTTTACTCAAAGGTATTTAACCTT
TCATCTAACAGGCATA
Found at i:174716 original size:20 final size:20
Alignment explanation
Indices: 174693--174759 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
174683 GTTTCCAAAT
*
174693 TCGCAACGCAAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
174713 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
* *
174733 CCGCAAAGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
*
174753 TAGCAAC
1 TCGCAAC
174760 ACAGAAGTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:174824 original size:19 final size:19
Alignment explanation
Indices: 174767--174897 Score: 176
Period size: 19 Copynumber: 6.7 Consensus size: 19
174757 AACACAGAAG
174767 TCAAATTCGCAAC-GCAATT
1 TCAAATTCGCAACTG-AATT
*
174786 TCCAAATTCCCAACACTGAATT
1 T-CAAATTCGC-A-ACTGAATT
174808 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
174827 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
174846 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
174865 TCAAATTCGCAACTCG-ATT
1 TCAAATTCGCAACT-GAATT
*
174884 TCCGAATTCGCAAC
1 T-CAAATTCGCAAC
174898 AGGTTTTAGA
Statistics
Matches: 103, Mismatches: 3, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
19 65 0.63
20 21 0.20
21 9 0.09
22 7 0.07
23 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.10, T:0.29
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:175073 original size:14 final size:15
Alignment explanation
Indices: 175054--175091 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
175044 TCCCTATCTC
175054 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
175068 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
175084 TAATTTTT
1 TAATTTTT
175092 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:175707 original size:12 final size:12
Alignment explanation
Indices: 175686--175719 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
175676 GCCACATTTC
*
175686 CAATACCAAACA
1 CAATATCAAACA
175698 CAATATCAAACA
1 CAATATCAAACA
*
175710 CAATCTCAAA
1 CAATATCAAA
175720 AGCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:178178 original size:18 final size:18
Alignment explanation
Indices: 178155--178189 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
178145 AGCAAAAGGG
*
178155 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
178173 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
178190 CAACCGACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:178474 original size:14 final size:14
Alignment explanation
Indices: 178455--178481 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
178445 GAATGTCAAA
178455 TTCGCATTGCGATT
1 TTCGCATTGCGATT
178469 TTCGCATTGCGAT
1 TTCGCATTGCGAT
178482 AGTCAAATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (14 bp):
TTCGCATTGCGATT
Found at i:178487 original size:34 final size:33
Alignment explanation
Indices: 178441--178534 Score: 107
Period size: 34 Copynumber: 2.8 Consensus size: 33
178431 GTTACGACTG
**
178441 TTGCGAATGTCAAATTCGCATTGCGATTTTCGCA
1 TTGCGAA-GTCAAATTCGCAACGCGATTTTCGCA
* *
178475 TTGCGATAGTCAAATTCGCAACGTGATTTTCGCG
1 TTGCGA-AGTCAAATTCGCAACGCGATTTTCGCA
* *
178509 TTGCGAAAGTCAAATTTGAAACGCGA
1 TTGCG-AAGTCAAATTCGCAACGCGA
178535 AATCAGAAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
34 49 0.96
35 2 0.04
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (33 bp):
TTGCGAAGTCAAATTCGCAACGCGATTTTCGCA
Found at i:178791 original size:64 final size:64
Alignment explanation
Indices: 178687--178847 Score: 259
Period size: 64 Copynumber: 2.5 Consensus size: 64
178677 CAAATTGAAT
*
178687 TTAAACAAATCAACTTTTACAAATCAATTAAACAACCAAAAAATATTTCTTATTTACACATCAA
1 TTAAACAAATCAACTTTTACAAATCAATTAAACAACCAAAAAATAATTCTTATTTACACATCAA
* * * *
178751 TTAAACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCGTCAA
1 TTAAACAAATCAACTTTTACAAATCAATTAAACAACCAAAAAATAATTCTTATTTACACATCAA
*
178815 TTAAATAAATCAACTTTTACAAATCAATGTAAA
1 TTAAACAAATCAACTTTTACAAATCAAT-TAAA
178848 ATTCAATTAA
Statistics
Matches: 90, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
64 86 0.96
65 4 0.04
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (64 bp):
TTAAACAAATCAACTTTTACAAATCAATTAAACAACCAAAAAATAATTCTTATTTACACATCAA
Found at i:180203 original size:21 final size:21
Alignment explanation
Indices: 180177--180295 Score: 114
Period size: 21 Copynumber: 5.7 Consensus size: 21
180167 GTGAATCGGG
* * *
180177 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGAGAGGGGC
* * *
180198 CTCTTGAATGATGACAGAGGC
1 CTCTTGAACGATGAGAGGGGC
* *
180219 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
180240 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
** *
180261 CTCTTCCACGAT-AGGAGGCGC
1 CTCTTGAACGATGA-GAGGGGC
*
180282 CTCTTGAATGATGA
1 CTCTTGAACGATGA
180296 CAGGTGAATA
Statistics
Matches: 77, Mismatches: 19, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
20 1 0.01
21 75 0.97
22 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:180224 original size:42 final size:41
Alignment explanation
Indices: 180177--180298 Score: 154
Period size: 42 Copynumber: 2.9 Consensus size: 41
180167 GTGAATCGGG
180177 CTCTTGAACGGTGGGAGGGACCTCTTGAATGATGACAGAGGC
1 CTCTTGAACGGTGGGAGGG-CCTCTTGAATGATGACAGAGGC
* * *
180219 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGGTGGGA-GGGCCTCTTGAATGATGACAGAGGC
** * *
180261 CTCTTCCACGATAGGAGGCGCCTCTTGAATGATGACAG
1 CTCTTGAACGGTGGGAGG-GCCTCTTGAATGATGACAG
180299 GTGAATAATG
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 2 0.03
42 64 0.93
43 3 0.04
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.21
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGCCTCTTGAATGATGACAGAGGC
Found at i:180659 original size:63 final size:63
Alignment explanation
Indices: 180592--180711 Score: 152
Period size: 63 Copynumber: 1.9 Consensus size: 63
180582 TAGAGCGGCT
* *
180592 ACCTCATCACGTAAAG-TAGATACCTCACCACGTAAAGCACCATTGTCATCACGTAAAACATCC
1 ACCTCACCACGTAAAGATAG-TACCTCACCACGCAAAGCACCATTGTCATCACGTAAAACATCC
* ** * * *
180655 ACCTCACCACGTAAAGATTGTACCTCATTACGCCATGCACCATTGTCTTCACGTAAA
1 ACCTCACCACGTAAAGATAGTACCTCACCACGCAAAGCACCATTGTCATCACGTAAA
180712 GTACCGACCT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 46 0.96
64 2 0.04
ACGTcount: A:0.33, C:0.32, G:0.12, T:0.23
Consensus pattern (63 bp):
ACCTCACCACGTAAAGATAGTACCTCACCACGCAAAGCACCATTGTCATCACGTAAAACATCC
Found at i:180665 original size:21 final size:20
Alignment explanation
Indices: 180613--180669 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
180603 TAAAGTAGAT
*
180613 ACCTCACCACGTAAAGCACC
1 ACCTCACCACGTAAAACACC
** *
180633 ATTGTCATCACGTAAAACATCC
1 A-CCTCACCACGTAAAACA-CC
180655 ACCTCACCACGTAAA
1 ACCTCACCACGTAAA
180670 GATTGTACCT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 1 0.04
21 24 0.86
22 3 0.11
ACGTcount: A:0.37, C:0.37, G:0.09, T:0.18
Consensus pattern (20 bp):
ACCTCACCACGTAAAACACC
Found at i:182553 original size:20 final size:20
Alignment explanation
Indices: 182492--182545 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
182482 CATCGTGAAC
182492 ATGAAAATCGCAACGCGAAA
1 ATGAAAATCGCAACGCGAAA
*
182512 AAGAAAATCGCAACGCGAAA
1 ATGAAAATCGCAACGCGAAA
182532 ATGAAAATCGCAAC
1 ATGAAAATCGCAAC
182546 AACAAAATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.52, C:0.20, G:0.19, T:0.09
Consensus pattern (20 bp):
ATGAAAATCGCAACGCGAAA
Found at i:182553 original size:54 final size:54
Alignment explanation
Indices: 182445--182565 Score: 138
Period size: 54 Copynumber: 2.3 Consensus size: 54
182435 GAACTTAAAT
* * * * * **
182445 TCGCAACACGAAAATGAAAATCACAACGCAAAAATCACATCGTGAACATGAAAA
1 TCGCAACGCGAAAAAGAAAATCACAACGCAAAAATAAAATCGTCAACAACAAAA
* *
182499 TCGCAACGCGAAAAAGAAAATCGCAACGCGAAAATGAAAATCG-CAACAACAAAA
1 TCGCAACGCGAAAAAGAAAATCACAACGCAAAAAT-AAAATCGTCAACAACAAAA
182553 TCGCAACGC-AAAA
1 TCGCAACGCGAAAA
182566 CTAAATTCAT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
53 4 0.07
54 48 0.84
55 5 0.09
ACGTcount: A:0.52, C:0.23, G:0.15, T:0.10
Consensus pattern (54 bp):
TCGCAACGCGAAAAAGAAAATCACAACGCAAAAATAAAATCGTCAACAACAAAA
Found at i:182605 original size:14 final size:14
Alignment explanation
Indices: 182588--182621 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
182578 TGCGATTTTC
*
182588 ATTTTCGCGTTGTG
1 ATTTTCGCGTTGCG
*
182602 ATTTTCGTGTTGCG
1 ATTTTCGCGTTGCG
182616 ATTTTC
1 ATTTTC
182622 ATTTTTGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.15, G:0.24, T:0.53
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:182646 original size:21 final size:20
Alignment explanation
Indices: 182602--182646 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
182592 TCGCGTTGTG
**
182602 ATTTTCGTGTTGCGATTTTC
1 ATTTTCGTGTTGCGATTTAA
*
182622 ATTTTTGTGTTGCGAATTTAA
1 ATTTTCGTGTTGCG-ATTTAA
182643 ATTT
1 ATTT
182647 CAAAAACTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.56
Consensus pattern (20 bp):
ATTTTCGTGTTGCGATTTAA
Found at i:183177 original size:20 final size:20
Alignment explanation
Indices: 183152--183202 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
183142 TAAACGTACT
183152 TTGCGAATTTGAC-TTCTGTG
1 TTGCGAATTTGACATTC-GTG
183172 TTGCG-ATTT-ACAAATTCGTG
1 TTGCGAATTTGAC--ATTCGTG
183192 TTGCGAATTTG
1 TTGCGAATTTG
183203 GAAACTGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
18 2 0.08
19 4 0.15
20 13 0.50
21 7 0.27
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.43
Consensus pattern (20 bp):
TTGCGAATTTGACATTCGTG
Found at i:187390 original size:29 final size:28
Alignment explanation
Indices: 187329--187509 Score: 123
Period size: 29 Copynumber: 6.3 Consensus size: 28
187319 ACCGTTGACC
****
187329 GGTGCTATTCTGGGAATTAATTCGATTTT
1 GGTGCTATTCTGGGAATTAATTC-AAAAG
*
187358 GGTGCTATTCTGGGAATTAATTCAAAGTG
1 GGTGCTATTCTGGGAATTAATTCAAA-AG
* * * * *
187387 GGTGCTATTTTGGTAATT-TTTTAAAAA
1 GGTGCTATTCTGGGAATTAATTCAAAAG
* * * *
187414 AGTGATATTCTTGGAATTAATTCAAAATT
1 GGTGCTATTCTGGGAATTAATTCAAAA-G
*
187443 GGTGCTATT-TAAGGAATTAATTCGAAAAG
1 GGTGCTATTCT-GGGAATTAATTC-AAAAG
* * * *
187472 GGTGCTATTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTCTGGGAATTA-ATTCAAAAG
187501 GGTGCTATT
1 GGTGCTATT
187510 TGTGTAAAAT
Statistics
Matches: 120, Mismatches: 25, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
27 13 0.11
28 13 0.11
29 87 0.73
30 7 0.06
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (28 bp):
GGTGCTATTCTGGGAATTAATTCAAAAG
Found at i:187471 original size:56 final size:56
Alignment explanation
Indices: 187363--187510 Score: 136
Period size: 56 Copynumber: 2.6 Consensus size: 56
187353 ATTTTGGTGC
* * **
187363 TATTCTGGGAATTAATTCAAAGTGGGTGCTATTTTGGTAATTTTTTAAAAAAGTGA
1 TATTCTGGGAATTAATTCAAAATGGGTGCTATTTAGGTAATTAATTAAAAAAGTGA
* * ** *
187419 TATTCTTGGAATTAATTCAAAATTGGTGCTATTTAAGG-AATTAATTCGAAAAGGGTGC
1 TATTCTGGGAATTAATTCAAAATGGGTGCTATTT-AGGTAATTAATT--AAAAAAGTGA
* * * * *
187477 TATTTTGGTAATTATTTTAAAAAGGGTGCTATTT
1 TATTCTGGGAATTAATTCAAAATGGGTGCTATTT
187511 GTGTAAAATG
Statistics
Matches: 73, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
56 37 0.51
57 2 0.03
58 34 0.47
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.41
Consensus pattern (56 bp):
TATTCTGGGAATTAATTCAAAATGGGTGCTATTTAGGTAATTAATTAAAAAAGTGA
Found at i:187477 original size:85 final size:86
Alignment explanation
Indices: 187334--187499 Score: 239
Period size: 85 Copynumber: 1.9 Consensus size: 86
187324 TGACCGGTGC
* ** * *
187334 TATTCTGGGAATTAATTCGATTTTGGTGCTATTCTGGGAATTAATTCAAAGTGGGTGCTATTTTG
1 TATTCTGGGAATTAATTCAAAATTGGTGCTATTCTAGGAATTAATTCAAAGAGGGTGCTATTTTG
187399 GTAATT-TTTTAAAAAAGTGA
66 GTAATTATTTTAAAAAAGTGA
*
187419 TATTCTTGGAATTAATTCAAAATTGGTGCTATT-TAAGGAATTAATTCGAAA-AGGGTGCTATTT
1 TATTCTGGGAATTAATTCAAAATTGGTGCTATTCT-AGGAATTAATTC-AAAGAGGGTGCTATTT
187482 TGGTAATTATTTTAAAAA
64 TGGTAATTATTTTAAAAA
187500 GGGTGCTATT
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
84 1 0.01
85 59 0.82
86 12 0.17
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.42
Consensus pattern (86 bp):
TATTCTGGGAATTAATTCAAAATTGGTGCTATTCTAGGAATTAATTCAAAGAGGGTGCTATTTTG
GTAATTATTTTAAAAAAGTGA
Found at i:187510 original size:29 final size:28
Alignment explanation
Indices: 187358--187510 Score: 130
Period size: 29 Copynumber: 5.4 Consensus size: 28
187348 ATTCGATTTT
* **
187358 GGTGCTATTCTGGGAATTAATTCAAAGTG
1 GGTGCTATT-TTGGAATTAATTCAAAAAG
* *
187387 GGTGCTATTTTGGTAATT-TTTTAAAAA-
1 GGTGCTATTTTGG-AATTAATTCAAAAAG
* * **
187414 AGTGATATTCTTGGAATTAATTCAAAATT
1 GGTGCTATT-TTGGAATTAATTCAAAAAG
* *
187443 GGTGCTATTTAAGGAATTAATTCGAAAAG
1 GGTGCTATTT-TGGAATTAATTCAAAAAG
* *
187472 GGTGCTATTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGG-AATTAATTCAAAAAG
187501 GGTGCTATTT
1 GGTGCTATTT
187511 GTGTAAAATG
Statistics
Matches: 98, Mismatches: 20, Indels: 12
0.75 0.15 0.09
Matches are distributed among these distances:
27 11 0.11
28 21 0.21
29 66 0.67
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.41
Consensus pattern (28 bp):
GGTGCTATTTTGGAATTAATTCAAAAAG
Found at i:193753 original size:30 final size:30
Alignment explanation
Indices: 193669--193774 Score: 97
Period size: 30 Copynumber: 3.5 Consensus size: 30
193659 TGAATTTAGG
* *
193669 GGTC-AATTCATATTTTATATAAAGTTTAA
1 GGTCAAATTAATATTTTATATAAATTTTAA
* * * *
193698 GAGTTAGATTAGTATTTTATGTAAATTTTAA
1 G-GTCAAATTAATATTTTATATAAATTTTAA
* * **
193729 GGTCAAATTAATATTTTGTCTAAATTTGGA
1 GGTCAAATTAATATTTTATATAAATTTTAA
*
193759 GGTCAAATTAAAATTT
1 GGTCAAATTAATATTT
193775 AACCATTTTT
Statistics
Matches: 61, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
29 1 0.02
30 39 0.64
31 21 0.34
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (30 bp):
GGTCAAATTAATATTTTATATAAATTTTAA
Found at i:194334 original size:17 final size:15
Alignment explanation
Indices: 194321--194349 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
194311 AAGATTATAG
194321 ATATATTATTATTAA
1 ATATATTATTATTAA
194336 ATATATTATT-TTAA
1 ATATATTATTATTAA
194350 TTATTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATATTATTATTAA
Found at i:203141 original size:45 final size:45
Alignment explanation
Indices: 203086--203226 Score: 149
Period size: 45 Copynumber: 3.0 Consensus size: 45
203076 ATCGATAAGA
* * *
203086 TTTCTTTAGTGACACCTTTTATGCCGATAATGCACCGTTATGCAT
1 TTTCATTAGTGACACCTTTTATGCCGAAAATGCACCATTATGCAT
* *
203131 TTTCATTAGTGGCACCTTTTATGTCGAAAATGCACCATTATGCATT
1 TTTCATTAGTGACACCTTTTATGCCGAAAATGCACCATTATGCA-T
* * * *
203177 TAACTTGCATTAGTGGCACATTTT-TGCCAAAAATGTACCATTATGCAT
1 T---TT-CATTAGTGACACCTTTTATGCCGAAAATGCACCATTATGCAT
203225 TT
1 TT
203227 AACTTGCATT
Statistics
Matches: 82, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
45 40 0.49
46 2 0.02
48 2 0.02
49 22 0.27
50 16 0.20
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (45 bp):
TTTCATTAGTGACACCTTTTATGCCGAAAATGCACCATTATGCAT
Done.