Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013215.1 Kokia drynarioides strain JFW-HI SEQ_128234, 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: 258192
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 117 characters in sequence are not A, C, G, or T
Found at i:36 original size:12 final size:12
Alignment explanation
Indices: 21--55 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
11 CAATACCTCC
21 ACCACCACCAAA
1 ACCACCACCAAA
* *
33 ACCACCACCTAG
1 ACCACCACCAAA
45 ACCACCACCAA
1 ACCACCACCAA
56 TGCCATGCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.43, C:0.51, G:0.03, T:0.03
Consensus pattern (12 bp):
ACCACCACCAAA
Found at i:1132 original size:2 final size:2
Alignment explanation
Indices: 1125--1150 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1115 GGATTGAAAA
1125 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1151 GCAAATTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1748 original size:22 final size:22
Alignment explanation
Indices: 1720--1764 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1710 ATATTCAAAC
*
1720 TTGACACTTTTTCTTAATTTGG
1 TTGACACTTTTTCTTAAGTTGG
1742 TTGACACTTTTTCTTAAGTTGG
1 TTGACACTTTTTCTTAAGTTGG
1764 T
1 T
1765 ATTTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.13, G:0.16, T:0.53
Consensus pattern (22 bp):
TTGACACTTTTTCTTAAGTTGG
Found at i:1789 original size:81 final size:81
Alignment explanation
Indices: 1660--1821 Score: 193
Period size: 81 Copynumber: 2.0 Consensus size: 81
1650 GTATCTAAAC
* * *** *
1660 TTGACACTTTTTTTTTAATTTGGTATTTAAATTTTTTTTTATTTAATTTGATA-TTCAAACTTGA
1 TTGACACTTTTTTCTTAAGTTGGTATTTAAATTTTTTGGGATTAAATTTGATACTT-AAACTTGA
*
1724 CACTTTTTCTTAATTTGG
65 CACTTTTT-TTAAATTGG
* * *
1742 TTGACAC-TTTTTCTTAAGTTGGTATTTAAATTTTTTGGGGTTAAATTTGGTACTTAAACTTGAT
1 TTGACACTTTTTTCTTAAGTTGGTATTTAAATTTTTTGGGATTAAATTTGATACTTAAACTTGAC
*
1806 TCTTTTTTTAAATTGG
66 ACTTTTTTTAAATTGG
1822 GTACCTAATC
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
80 8 0.12
81 51 0.75
82 9 0.13
ACGTcount: A:0.24, C:0.08, G:0.12, T:0.56
Consensus pattern (81 bp):
TTGACACTTTTTTCTTAAGTTGGTATTTAAATTTTTTGGGATTAAATTTGATACTTAAACTTGAC
ACTTTTTTTAAATTGG
Found at i:2124 original size:61 final size:62
Alignment explanation
Indices: 2001--2172 Score: 154
Period size: 61 Copynumber: 2.8 Consensus size: 62
1991 GAATCTTAAT
* * * * ** * *
2001 AAAAGTATAGGTACCAAATTAGGAAAAAAA-TGTTAAGTTCAGGCACCAAATTGGGTCCAAA
1 AAAAGTTTAGGTACAAAATTAGAAAAAAAAGTGTCAAGTTCAGATACCAAATTAGGTCAAAA
* * *
2062 AAAGGTTTAGGTACAAAATTAGAAAAAAAAGTGTCAAGTTCAGATATCAAATTATGT-AAAA
1 AAAAGTTTAGGTACAAAATTAGAAAAAAAAGTGTCAAGTTCAGATACCAAATTAGGTCAAAA
* * ** * * *
2123 AAAATTTTAAGTATTAAATT--AAGAAAAAGTGTCAAATTCAGATACGAAAT
1 AAAAGTTTAGGTACAAAATTAGAAAAAAAAGTGTCAAGTTCAGATACCAAAT
2173 ATTATATTAA
Statistics
Matches: 90, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
59 26 0.29
61 44 0.49
62 20 0.22
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.26
Consensus pattern (62 bp):
AAAAGTTTAGGTACAAAATTAGAAAAAAAAGTGTCAAGTTCAGATACCAAATTAGGTCAAAA
Found at i:5068 original size:16 final size:15
Alignment explanation
Indices: 5049--5083 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
5039 AATATATTTC
5049 TTTTTTC-TTTTATT
1 TTTTTTCTTTTTATT
5063 TTTTTTCTTTTTATT
1 TTTTTTCTTTTTATT
5078 TTTTTT
1 TTTTTT
5084 ATATGTGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTCTTTTTATT
Found at i:29775 original size:29 final size:29
Alignment explanation
Indices: 29733--29791 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
29723 CTTTTTGTCC
29733 TTCTAAACCTCCAAAATTGAGAAGAAGAG
1 TTCTAAACCTCCAAAATTGAGAAGAAGAG
29762 TTCTAAACCTCCAAAATTGAGAAGAAGAG
1 TTCTAAACCTCCAAAATTGAGAAGAAGAG
29791 T
1 T
29792 CGTACTTAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (29 bp):
TTCTAAACCTCCAAAATTGAGAAGAAGAG
Found at i:45126 original size:13 final size:13
Alignment explanation
Indices: 45108--45132 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45098 ATAAAACGAA
45108 CAAAAACAAAAAG
1 CAAAAACAAAAAG
45121 CAAAAACAAAAA
1 CAAAAACAAAAA
45133 ATGAACCCTA
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:0.80, C:0.16, G:0.04, T:0.00
Consensus pattern (13 bp):
CAAAAACAAAAAG
Found at i:63687 original size:17 final size:17
Alignment explanation
Indices: 63665--63697 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
63655 TTTTGCCACT
63665 AACT-AAACACAATACTA
1 AACTAAAACA-AATACTA
63682 AACTAAAACAAATACT
1 AACTAAAACAAATACT
63698 CACATGCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.61, C:0.21, G:0.00, T:0.18
Consensus pattern (17 bp):
AACTAAAACAAATACTA
Found at i:66741 original size:76 final size:76
Alignment explanation
Indices: 66607--66765 Score: 221
Period size: 76 Copynumber: 2.1 Consensus size: 76
66597 CTTTACCATC
* * * * *
66607 AACCAAATTCGTCAATTCGTAGCACCCAATGCCTAGCGGATAAACTGCGATAAGTGAGCCCAACT
1 AACCAACTTCGTCAATTCATAGCACCCAATGCCTAGCAGATAAACCGCGATAAATGAGCCCAACT
66672 CTAGTTGGATT
66 CTAGTTGGATT
* * * *
66683 AACCAACTTCCGTCAATTCATGGCACCCAGTGCCTAG-AGATAAACCGTGATAAATGAGCCCAGC
1 AACCAACTT-CGTCAATTCATAGCACCCAATGCCTAGCAGATAAACCGCGATAAATGAGCCCAAC
66747 TCTAGTTGGATT
65 TCTAGTTGGATT
66759 AACCAAC
1 AACCAAC
66766 AGTTTGCGCC
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
76 49 0.67
77 24 0.33
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (76 bp):
AACCAACTTCGTCAATTCATAGCACCCAATGCCTAGCAGATAAACCGCGATAAATGAGCCCAACT
CTAGTTGGATT
Found at i:74870 original size:22 final size:20
Alignment explanation
Indices: 74833--74872 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
74823 GAATTATATA
74833 TAAATAAGGTTAATTAAGGC
1 TAAATAAGGTTAATTAAGGC
74853 TAAATAAGTGATTAATTAAG
1 TAAATAAG-G-TTAATTAAG
74873 TTAATTATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (20 bp):
TAAATAAGGTTAATTAAGGC
Found at i:78669 original size:17 final size:17
Alignment explanation
Indices: 78639--78692 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
78629 ACTACAATGC
* *
78639 AAATGCACTAACAAATA
1 AAATGCAATGACAAATA
*
78656 AAATGCAATGACAAAGAA
1 AAATGCAATGACAAA-TA
* *
78674 AAATGTAATGACAACTA
1 AAATGCAATGACAAATA
78691 AA
1 AA
78693 TGCTATGCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.59, C:0.13, G:0.11, T:0.17
Consensus pattern (17 bp):
AAATGCAATGACAAATA
Found at i:78819 original size:19 final size:20
Alignment explanation
Indices: 78772--78819 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
78762 TTAGCTTTCT
* * *
78772 TCTTCTTCTTCTTTGGGCAC
1 TCTTTTTCTACTTTGCGCAC
*
78792 TCCTTTTCTACTTTGCGC-C
1 TCTTTTTCTACTTTGCGCAC
78811 TCTTTTTCT
1 TCTTTTTCT
78820 TGTCTTTCCT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.04, C:0.31, G:0.10, T:0.54
Consensus pattern (20 bp):
TCTTTTTCTACTTTGCGCAC
Found at i:103084 original size:30 final size:31
Alignment explanation
Indices: 103028--103089 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
103018 CACCGGACAG
103028 ATAGGAGAACATAAGTCTTAAAACATACTTT
1 ATAGGAGAACATAAGTCTTAAAACATACTTT
103059 ATAGGAGAACATAAGTCTT-AAACATACTTT
1 ATAGGAGAACATAAGTCTTAAAACATACTTT
103089 A
1 A
103090 CCAAATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (31 bp):
ATAGGAGAACATAAGTCTTAAAACATACTTT
Found at i:108484 original size:24 final size:24
Alignment explanation
Indices: 108447--108493 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
108437 CCGAAAATAT
*
108447 GAGGAGGAAGATAATGAAGAAGAC
1 GAGGAGGAAGATAAAGAAGAAGAC
*
108471 GAGGAAGGAA-ATAAAGAGGAAGA
1 GAGG-AGGAAGATAAAGAAGAAGA
108494 GAAAGAAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.53, C:0.02, G:0.38, T:0.06
Consensus pattern (24 bp):
GAGGAGGAAGATAAAGAAGAAGAC
Found at i:120175 original size:21 final size:20
Alignment explanation
Indices: 120149--120190 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 20
120139 TTCTTTTTTT
120149 TTCTTCTTCTTTCTTTCCATC
1 TTCTTCTTC-TTCTTTCCATC
120170 TTCTTCTTCTTCTTTCCATC
1 TTCTTCTTCTTCTTTCCATC
120190 T
1 T
120191 GTTACTGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.05, C:0.33, G:0.00, T:0.62
Consensus pattern (20 bp):
TTCTTCTTCTTCTTTCCATC
Found at i:124278 original size:59 final size:59
Alignment explanation
Indices: 124196--124366 Score: 209
Period size: 59 Copynumber: 2.9 Consensus size: 59
124186 AATTGAATCT
* * *
124196 TAAAAAAATTTAGGTACCAAATTAGAAAAAAATGTCAAGTTCAGGTACCAAATTGGGTC
1 TAAAAAAGTTTAGGTACCAAATTAGAAAAAAGTGTCAAGTTCAGGTACCAAATTGGGTA
* * * * * *
124255 TAAAAAAGTTTAGGTGCCGAATTAGGAAAAAGTGCCAAGTTCAGGTATCAATTTGGGTA
1 TAAAAAAGTTTAGGTACCAAATTAGAAAAAAGTGTCAAGTTCAGGTACCAAATTGGGTA
* * * *
124314 AAAAAAAGTTTAGGCACCAAATTA-AAAAACAGCGTCAAGTTCAGATACCAAAT
1 TAAAAAAGTTTAGGTACCAAATTAGAAAAA-AGTGTCAAGTTCAGGTACCAAAT
124367 GTTATATTAA
Statistics
Matches: 92, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
58 4 0.04
59 88 0.96
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (59 bp):
TAAAAAAGTTTAGGTACCAAATTAGAAAAAAGTGTCAAGTTCAGGTACCAAATTGGGTA
Found at i:133070 original size:27 final size:27
Alignment explanation
Indices: 133042--133110 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 27
133032 TTAAAAAATA
*
133042 AAAAATATATAAAATACAT-ATA-TTTT
1 AAAAATATATAAAATA-ATAAAATTTTT
*
133068 AAAAATATATTAAAATATTAAAATTTTTT
1 AAAAATATA-TAAAATAATAAAA-TTTTT
133097 AAAAATATATAAAA
1 AAAAATATATAAAA
133111 CCATTAAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
26 10 0.27
27 9 0.24
28 5 0.14
29 13 0.35
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (27 bp):
AAAAATATATAAAATAATAAAATTTTT
Found at i:133116 original size:29 final size:29
Alignment explanation
Indices: 133064--133123 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
133054 AATACATATA
*
133064 TTTTAAAAATATATTAAAATATTAAAATT
1 TTTTAAAAATATATTAAAACATTAAAATT
*
133093 TTTTAAAAATATA-TAAAACCATTAAACTT
1 TTTTAAAAATATATTAAAA-CATTAAAATT
133122 TT
1 TT
133124 AACTTTTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (29 bp):
TTTTAAAAATATATTAAAACATTAAAATT
Found at i:135470 original size:20 final size:20
Alignment explanation
Indices: 135445--135485 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
135435 ATAAATAGGA
135445 AAAGCTAGGGATTATTTTAC
1 AAAGCTAGGGATTATTTTAC
135465 AAAGCTAGGGATTATTTTAC
1 AAAGCTAGGGATTATTTTAC
135485 A
1 A
135486 TACTTTCATT
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:0.37, C:0.10, G:0.20, T:0.34
Consensus pattern (20 bp):
AAAGCTAGGGATTATTTTAC
Found at i:137148 original size:14 final size:14
Alignment explanation
Indices: 137129--137174 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
137119 AAGAATGAAC
137129 AAATATACGAAAAT
1 AAATATACGAAAAT
137143 AAATATGA-GAAAAAT
1 AAATAT-ACG-AAAAT
137158 AAA-ATACGAAAA-
1 AAATATACGAAAAT
137170 AAATA
1 AAATA
137175 AATGAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 3 0.11
13 6 0.21
14 10 0.36
15 9 0.32
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.17
Consensus pattern (14 bp):
AAATATACGAAAAT
Found at i:137158 original size:15 final size:15
Alignment explanation
Indices: 137138--137188 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
137128 CAAATATACG
137138 AAAATAAATATGAGA
1 AAAATAAATATGAGA
* *
137153 AAAATAAAATACGAAA
1 AAAAT-AAATATGAGA
137169 AAAAT-AA-ATGAG-
1 AAAATAAATATGAGA
137181 AAAATAAA
1 AAAATAAA
137189 AAATTAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
12 5 0.17
13 5 0.17
14 2 0.07
15 5 0.17
16 13 0.43
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.16
Consensus pattern (15 bp):
AAAATAAATATGAGA
Found at i:137184 original size:28 final size:28
Alignment explanation
Indices: 137133--137189 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
137123 ATGAACAAAT
137133 ATACGAAAATAAATATGAGAAAAATAAA
1 ATACGAAAATAAATATGAGAAAAATAAA
137161 ATACGAAAA-AAATAAATGAG-AAAATAAA
1 ATACGAAAATAAAT--ATGAGAAAAATAAA
137189 A
1 A
137190 AATTAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 4 0.15
28 18 0.67
29 5 0.19
ACGTcount: A:0.70, C:0.04, G:0.11, T:0.16
Consensus pattern (28 bp):
ATACGAAAATAAATATGAGAAAAATAAA
Found at i:137192 original size:15 final size:14
Alignment explanation
Indices: 137137--137192 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
137127 ACAAATATAC
* *
137137 GAAAATAAATATGA
1 GAAAAAAAAAATGA
*
137151 GAAAAATAAAAT-A
1 GAAAAAAAAAATGA
137164 CGAAAAAAATAAATGA
1 -GAAAAAAA-AAATGA
137180 GAAAATAAAAAAT
1 GAAAA-AAAAAAT
137193 TAATTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
13 1 0.03
14 16 0.47
15 13 0.38
16 4 0.12
ACGTcount: A:0.71, C:0.02, G:0.11, T:0.16
Consensus pattern (14 bp):
GAAAAAAAAAATGA
Found at i:137655 original size:30 final size:29
Alignment explanation
Indices: 137285--137661 Score: 239
Period size: 29 Copynumber: 12.9 Consensus size: 29
137275 GTTTGAGGTT
* * *
137285 AAATGTAATTTTGGAAAGTTTTAAGGGTAA
1 AAATGTGATTTTTGAAAG-TTTAGGGGTAA
* * * *
137315 AAATATTATTTTAGGAAAATTTA-GGGTAA
1 AAATGTGATTTT-TGAAAGTTTAGGGGTAA
* * * *
137344 AAACT-TGATTTTTGGAAGTTCAAGGGCAA
1 AAA-TGTGATTTTTGAAAGTTTAGGGGTAA
* * * *
137373 AAATATGATTTTTGGAAGTTTA-AGGCAA
1 AAATGTGATTTTTGAAAGTTTAGGGGTAA
* *
137401 AAATGTGATTTTTGGAAGTTTGGGGGTAA
1 AAATGTGATTTTTGAAAGTTTAGGGGTAA
* *
137430 AAATGTGATTTTTGAAAGTTTAGGAGCAA
1 AAATGTGATTTTTGAAAGTTTAGGGGTAA
* * * *
137459 AAATGTAATTTTTGTAAG-TTCGGGGGAA
1 AAATGTGATTTTTGAAAGTTTAGGGGTAA
* * *
137487 AAATGTAATTTTTGAGAAG-TTCGGAAGTAA
1 AAATGTGATTTTTGA-AAGTTTAGG-GGTAA
* * * * *
137517 AAATATAATTTTTGGAAG-TTCGAGGATAA
1 AAATGTGATTTTTGAAAGTTTAG-GGGTAA
* * ** *
137546 GAATGT-ATTTTTTGGAAGTTCGGGGGTTA
1 AAATGTGA-TTTTTGAAAGTTTAGGGGTAA
*
137575 AAATGTGATTTTTGGAAAGTTTATGGGTAA
1 AAATGTGATTTTT-GAAAGTTTAGGGGTAA
* *
137605 AAATGTAATTTTTGAGAAGTTT-GGGGATCA
1 AAATGTGATTTTTGA-AAGTTTAGGGG-TAA
*
137635 AAATATGATTTTTGTAAAGTTTAGGGG
1 AAATGTGATTTTTG-AAAGTTTAGGGG
137662 CCTATTGAGC
Statistics
Matches: 283, Mismatches: 48, Indels: 31
0.78 0.13 0.09
Matches are distributed among these distances:
28 54 0.19
29 135 0.48
30 84 0.30
31 10 0.04
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (29 bp):
AAATGTGATTTTTGAAAGTTTAGGGGTAA
Found at i:140688 original size:57 final size:57
Alignment explanation
Indices: 140600--140713 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
140590 AAATAACATG
140600 TATAGACTAGTTTAAGGTTGTTAATAATGTGTTTGTAATGTATTTAATGTGAATTCA
1 TATAGACTAGTTTAAGGTTGTTAATAATGTGTTTGTAATGTATTTAATGTGAATTCA
140657 TATAGACTAGTTTAAGGTTGTTAATAATGTGTTTGTAATGTATTTAATGTGAATTCA
1 TATAGACTAGTTTAAGGTTGTTAATAATGTGTTTGTAATGTATTTAATGTGAATTCA
140714 AAGTGTCAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.46
Consensus pattern (57 bp):
TATAGACTAGTTTAAGGTTGTTAATAATGTGTTTGTAATGTATTTAATGTGAATTCA
Found at i:145792 original size:48 final size:47
Alignment explanation
Indices: 145739--145914 Score: 180
Period size: 48 Copynumber: 3.7 Consensus size: 47
145729 GGGTATATTT
*
145739 GTTGTGTTTGAAGGGTATACTTGGTTGTGTTCGGAGGTTATATATATG
1 GTTGTGTTTGAAGGGTATA-TTGGTTGTGTTTGGAGGTTATATATATG
* *
145787 GTTGTGTTT-AGAGGGTACATATGGTTGTGTTTAGAGGTTATATATATG
1 GTTGTGTTTGA-AGGGTATAT-TGGTTGTGTTTGGAGGTTATATATATG
* * * *
145835 GTTGTGTTTTG-AGGGTATATTTTGTTGTGTTTGGAGG--GTACATACG
1 GTTGTG-TTTGAAGGGTATA-TTGGTTGTGTTTGGAGGTTATATATATG
* * *
145881 GTTATGTTTGGAGGTTATGATTGGTTGTGTTTGG
1 GTTGTGTTTGAAGGGTAT-ATTGGTTGTGTTTGG
145915 TGGGTGATAG
Statistics
Matches: 109, Mismatches: 12, Indels: 16
0.80 0.09 0.12
Matches are distributed among these distances:
45 4 0.04
46 30 0.28
47 3 0.03
48 68 0.62
49 4 0.04
ACGTcount: A:0.18, C:0.03, G:0.34, T:0.45
Consensus pattern (47 bp):
GTTGTGTTTGAAGGGTATATTGGTTGTGTTTGGAGGTTATATATATG
Found at i:145854 original size:71 final size:69
Alignment explanation
Indices: 145779--145912 Score: 187
Period size: 71 Copynumber: 1.9 Consensus size: 69
145769 TCGGAGGTTA
* * *
145779 TATATATGGTTGTGTTTAGAGGGTACATATGGTTGTGTTTAGAGGTTATATATATGGTTGTGTTT
1 TATATATGGTTGTGTTTAGAGGGTACATACGGTTATGTTTAGAGGTTAT-GAT-TGGTTGTGTTT
145844 TGAGGG
64 TGAGGG
* * * *
145850 TATATTTTGTTGTGTTTGGAGGGTACATACGGTTATGTTTGGAGGTTATGATTGGTTGTGTTT
1 TATATATGGTTGTGTTTAGAGGGTACATACGGTTATGTTTAGAGGTTATGATTGGTTGTGTTT
145913 GGTGGGTGAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
69 11 0.20
70 2 0.04
71 43 0.77
ACGTcount: A:0.19, C:0.02, G:0.32, T:0.47
Consensus pattern (69 bp):
TATATATGGTTGTGTTTAGAGGGTACATACGGTTATGTTTAGAGGTTATGATTGGTTGTGTTTTG
AGGG
Found at i:145914 original size:23 final size:23
Alignment explanation
Indices: 145728--145919 Score: 165
Period size: 23 Copynumber: 8.2 Consensus size: 23
145718 GATATGTTGA
* *
145728 AGGGTATAT-TTGTTGTGTTTGA
1 AGGGTATATATGGTTGTGTTTGG
*
145750 AGGGTATACT-TGGTTGTGTTCGG
1 AGGGTATA-TATGGTTGTGTTTGG
* *
145773 AGGTTATATATATGGTTGTGTTTAG
1 AGG--GTATATATGGTTGTGTTTGG
* *
145798 AGGGTACATATGGTTGTGTTTAG
1 AGGGTATATATGGTTGTGTTTGG
* *
145821 AGGTTATATATATGGTTGTGTTTTG
1 AGG--GTATATATGGTTGTGTTTGG
* *
145846 AGGGTATATTTTGTTGTGTTTGG
1 AGGGTATATATGGTTGTGTTTGG
* * *
145869 AGGGTACATACGGTTATGTTTGG
1 AGGGTATATATGGTTGTGTTTGG
*
145892 AGGTTATGAT-TGGTTGTGTTTGG
1 AGGGTAT-ATATGGTTGTGTTTGG
*
145915 TGGGT
1 AGGGT
145920 GATAGTTTTA
Statistics
Matches: 137, Mismatches: 26, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
22 8 0.06
23 88 0.64
24 3 0.02
25 38 0.28
ACGTcount: A:0.18, C:0.03, G:0.34, T:0.45
Consensus pattern (23 bp):
AGGGTATATATGGTTGTGTTTGG
Found at i:153760 original size:4 final size:4
Alignment explanation
Indices: 153751--153777 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
153741 GTATAATAAT
153751 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
153778 TATATATATA
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:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:154873 original size:3 final size:3
Alignment explanation
Indices: 154865--154909 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
154855 CGGGGCAACA
*
154865 TCT TCT TCT TTT TCT TCT TCT T-T TCTT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT
154910 GCCTCAATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:159141 original size:40 final size:40
Alignment explanation
Indices: 159043--159121 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
159033 TTACGATCTA
159043 GTTGTATCCAGAGTATCCATCAAGGAAATAGTAATAGGCC
1 GTTGTATCCAGAGTATCCATCAAGGAAATAGTAATAGGCC
159083 GTTGTATCCAGAGTATCCATCAAGGAAATAGTAATAGGC
1 GTTGTATCCAGAGTATCCATCAAGGAAATAGTAATAGGC
159122 TTTACCAGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.25
Consensus pattern (40 bp):
GTTGTATCCAGAGTATCCATCAAGGAAATAGTAATAGGCC
Found at i:162745 original size:24 final size:24
Alignment explanation
Indices: 162712--162758 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
162702 GTCAAGAGCA
*
162712 AAAATTGTCAGTGCAAATGTAATAT
1 AAAATTGTCAGAGCAAAT-TAATAT
162737 AAAA-TGTCAGAGCAAATTAATA
1 AAAATTGTCAGAGCAAATTAATA
162759 AAAGATGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.28
Consensus pattern (24 bp):
AAAATTGTCAGAGCAAATTAATAT
Found at i:175835 original size:5 final size:5
Alignment explanation
Indices: 175825--175863 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
175815 TTTCAATTTT
175825 TAAAA TAAAA TAAAA TTAAAA T-AAA T-AAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA -TAAAA TAAAA TAAAA TAAAA TAAAA
175864 ATACTCAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 8 0.25
5 19 0.59
6 5 0.16
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:175854 original size:19 final size:20
Alignment explanation
Indices: 175827--175866 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
175817 TCAATTTTTA
*
175827 AAATAAAATAAAATTAAAAT
1 AAATAAAATAAAATAAAAAT
175847 AAAT-AAATAAAATAAAAAT
1 AAATAAAATAAAATAAAAAT
175866 A
1 A
175867 CTCAGGTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
AAATAAAATAAAATAAAAAT
Found at i:188670 original size:112 final size:112
Alignment explanation
Indices: 188513--188729 Score: 346
Period size: 112 Copynumber: 1.9 Consensus size: 112
188503 AATGTTTGTC
*
188513 ATTTTTAATATTTTCATTCATACGAGCTTCGCCACCAATAAAATTCAATTTTATCCACCTTACAA
1 ATTTTTAATATTTCCATTCATACGAGCTTCGCCACCAATAAAATTCAATTTTATCCACCTTACAA
*
188578 CCTTGTTCAAGCATTTTTGCATCGAAATAACGGTTAGTGGACCAATG
66 CCCTGTTCAAGCATTTTTGCATCGAAATAACGGTTAGTGGACCAATG
* * * *
188625 ATTTTTATTCTTTCCATTCA-AGCGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACA
1 ATTTTTAATATTTCCATTCATA-CGAGCTTCGCCACCAATAAAATTCAATTTTATCCACCTTACA
* *
188689 ACCCTGTTCAAGCATTTTTGCATTGAAATGACGGTTAGTGG
65 ACCCTGTTCAAGCATTTTTGCATCGAAATAACGGTTAGTGG
188730 TCTAACGGTA
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
111 1 0.01
112 95 0.99
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (112 bp):
ATTTTTAATATTTCCATTCATACGAGCTTCGCCACCAATAAAATTCAATTTTATCCACCTTACAA
CCCTGTTCAAGCATTTTTGCATCGAAATAACGGTTAGTGGACCAATG
Found at i:189377 original size:49 final size:49
Alignment explanation
Indices: 189160--189736 Score: 317
Period size: 49 Copynumber: 11.8 Consensus size: 49
189150 GAAAACATAG
* * *
189160 AGATATGAAGGGAAAGGTTGAGGCCGTAATGGCGAA-CTCGGTACCTTAGA
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCT-GGTACCAT-GA
* * * * ** * * *
189210 AGACATGATGGGAAA-GATCACGGTTGTAACGG-TAGATCTAGTACCATG-
1 AGATATGAAGGGAAAGGTTGA-GGCCGCAACGGCGA-ATCTGGTACCATGA
* * * * *
189258 -GATATGAAGAGAAAGGTTGAGGTCGCAATGGCGAACCCGGTACCATAGA
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCTGGTACCAT-GA
* * * *
189307 AGATGTGATGGGAAAGATTGAGGCCGCAATGGCGAATCTGGTACCATGA
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCTGGTACCATGA
* * * ** *
189356 AGATATGAAGGGAAAGGTTGAGGCTGTAACGGTGAA-C---CCCCTTAGA
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCTGGTACCAT-GA
* * * *
189402 AGA-AGTGATGGG-AAGGATTGAGGCCGCAACAGCGAATCCGATACCATGA
1 AGATA-TGAAGGGAAAGG-TTGAGGCCGCAACGGCGAATCTGGTACCATGA
* * *
189451 AGATATGAAGGGAAATGTTGAGGCAGCAACGGCGAA-CTTGGTACCTTAGA
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAATC-TGGTACCAT-GA
* * * * * *
189501 AGATGTGATGGG-AAGGATTGAAGCCGTAATGACGAAT-TGGGTACCATGA
1 AGATATGAAGGGAAAGG-TTGAGGCCGCAACGGCGAATCT-GGTACCATGA
** * * *
189550 AGATATGAAGGGAAAGGTTGAGGCCGCAACGATGAACCCGGTACC-TCAGC
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCTGGTACCAT--GA
* * * * * *
189600 AGATGTGATGGG-AAGGATTGAGGCCGCAACGACGAATCTTGTATCATGG
1 AGATATGAAGGGAAAGG-TTGAGGCCGCAACGGCGAATCTGGTACCATGA
* ** * * * ** *
189649 AGATATGGAGGGAAAGGTTGAAACCGCAACGACAAACCTTATACC-TTA
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCTGGTACCATGA
* *
189697 GAGATATGAAGGGAAAGAG-TGAGGCCGCAATGACGAATCT
1 -AGATATGAAGGGAAAG-GTTGAGGCCGCAACGGCGAATCT
189737 CATACCCTAA
Statistics
Matches: 399, Mismatches: 97, Indels: 63
0.71 0.17 0.11
Matches are distributed among these distances:
45 8 0.02
46 26 0.07
47 29 0.07
48 9 0.02
49 174 0.44
50 150 0.38
51 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.32, T:0.19
Consensus pattern (49 bp):
AGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCTGGTACCATGA
Found at i:189503 original size:194 final size:194
Alignment explanation
Indices: 189245--189736 Score: 577
Period size: 194 Copynumber: 2.5 Consensus size: 194
189235 GTAACGGTAG
* * * ** *
189245 ATCTAGTACCATG-GATATGAAGAGAAAGGTTGAGGTCGCAATGGCGAACCCGGTACCATAGAAG
1 ATCTCGTACCATGAGATATGAAGGGAAAGGTTGAGG-CGCAACGGCGAACTTGGTACCTTAGAAG
*
189309 ATGTGATGGGAAAGATTGAGGCCGCAATGGCGAATCT-GGTACCATGAAGATATGAAGGGAAAGG
65 ATGTGATGGGAAAGATTGAGGCCGCAATGACGAATCTGGGTACCATGAAGATATGAAGGGAAAGG
* * * *
189373 TTGAGGCTGTAACGGTGAACCC-CCTTAGAAGAAGTGATGGGAAGGATTGAGGCCGCAAC-AGCG
130 TTGAGGCCGCAACGATGAACCCGCCTCAGAAGAAGTGATGGGAAGGATTGAGGCCGCAACGA-CG
189436 A
194 A
*
189437 ATC-CGATACCATGAAGATATGAAGGGAAATGTTGAGGCAGCAACGGCGAACTTGGTACCTTAGA
1 ATCTCG-TACCATG-AGATATGAAGGGAAAGGTTGAGGC-GCAACGGCGAACTTGGTACCTTAGA
* * *
189501 AGATGTGATGGGAAGGATTGAAGCCGTAATGACGAAT-TGGGTACCATGAAGATATGAAGGGAAA
63 AGATGTGATGGGAAAGATTGAGGCCGCAATGACGAATCTGGGTACCATGAAGATATGAAGGGAAA
* *
189565 GGTTGAGGCCGCAACGATGAACCCGGTACCTCAGCAGATGTGATGGGAAGGATTGAGGCCGCAAC
128 GGTTGAGGCCGCAACGATGAACCC-G--CCTCAGAAGAAGTGATGGGAAGGATTGAGGCCGCAAC
189630 GACGA
190 GACGA
* * * ** * * *
189635 ATCTTGTATCATGGAGATATGGAGGGAAAGGTTGAAACCGCAACGACAAACCTT-ATACCTTAG-
1 ATCTCGTACCAT-GAGATATGAAGGGAAAGGTTG-AGGCGCAACGGCGAA-CTTGGTACCTTAGA
* * *
189698 AGATATGAAGGGAAAGAGTGAGGCCGCAATGACGAATCT
63 AGATGTGATGGGAAAGATTGAGGCCGCAATGACGAATCT
189737 CATACCCTAA
Statistics
Matches: 253, Mismatches: 32, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
191 1 0.00
192 10 0.04
193 2 0.01
194 120 0.47
197 31 0.12
198 81 0.32
199 8 0.03
ACGTcount: A:0.34, C:0.16, G:0.32, T:0.19
Consensus pattern (194 bp):
ATCTCGTACCATGAGATATGAAGGGAAAGGTTGAGGCGCAACGGCGAACTTGGTACCTTAGAAGA
TGTGATGGGAAAGATTGAGGCCGCAATGACGAATCTGGGTACCATGAAGATATGAAGGGAAAGGT
TGAGGCCGCAACGATGAACCCGCCTCAGAAGAAGTGATGGGAAGGATTGAGGCCGCAACGACGA
Found at i:189546 original size:99 final size:98
Alignment explanation
Indices: 189160--189736 Score: 539
Period size: 99 Copynumber: 5.9 Consensus size: 98
189150 GAAAACATAG
* * * ** *
189160 AGATATGAAGGGAAAGGTTGAGGCCGTAATGGCGAACTCGGTACCTTAGAAGACATGATGGGAAA
1 AGATATGAAGGGAAAGGTTGAGG-CGCAACGGCGAACCCGGTACCTTAGAAGATGTGATGGGAAG
* ** * * *
189225 GA-TCACGGTTGTAACG--GTAGATCTAGTACCATG-
65 GATTGA-GGCCGCAATGACG-A-ATCTGGTACCATGA
* * * *
189258 -GATATGAAGAGAAAGGTTGAGGTCGCAATGGCGAACCCGGTACCATAGAAGATGTGATGGGAAA
1 AGATATGAAGGGAAAGGTTGAGG-CGCAACGGCGAACCCGGTACCTTAGAAGATGTGATGGGAAG
*
189322 GATTGAGGCCGCAATGGCGAATCTGGTACCATGA
65 GATTGAGGCCGCAATGACGAATCTGGTACCATGA
* * *
189356 AGATATGAAGGGAAAGGTTGAGGCTGTAACGGTGAACCC----CCTTAGAAGAAGTGATGGGAAG
1 AGATATGAAGGGAAAGGTTGAGGC-GCAACGGCGAACCCGGTACCTTAGAAGATGTGATGGGAAG
* * *
189417 GATTGAGGCCGCAA-CAGCGAATCCGATACCATGA
65 GATTGAGGCCGCAATGA-CGAATCTGGTACCATGA
* **
189451 AGATATGAAGGGAAATGTTGAGGCAGCAACGGCGAACTTGGTACCTTAGAAGATGTGATGGGAAG
1 AGATATGAAGGGAAAGGTTGAGGC-GCAACGGCGAACCCGGTACCTTAGAAGATGTGATGGGAAG
* *
189516 GATTGAAGCCGTAATGACGAAT-TGGGTACCATGA
65 GATTGAGGCCGCAATGACGAATCT-GGTACCATGA
** * *
189550 AGATATGAAGGGAAAGGTTGAGGCCGCAACGATGAACCCGGTACCTCAGCAGATGTGATGGGAAG
1 AGATATGAAGGGAAAGGTTGAGG-CGCAACGGCGAACCCGGTACCTTAGAAGATGTGATGGGAAG
* * * *
189615 GATTGAGGCCGCAACGACGAATCTTGTATCATGG
65 GATTGAGGCCGCAATGACGAATCTGGTACCATGA
* ** * * *** * * *
189649 AGATATGGAGGGAAAGGTTGAAACCGCAACGACAAACCTTATACCTTAG-AGATATGAAGGGAAA
1 AGATATGAAGGGAAAGGTTG-AGGCGCAACGGCGAACCCGGTACCTTAGAAGATGTGATGGGAAG
*
189713 GAGTGAGGCCGCAATGACGAATCT
65 GATTGAGGCCGCAATGACGAATCT
189737 CATACCCTAA
Statistics
Matches: 400, Mismatches: 63, Indels: 32
0.81 0.13 0.06
Matches are distributed among these distances:
95 81 0.20
97 77 0.19
98 38 0.09
99 200 0.50
100 4 0.01
ACGTcount: A:0.33, C:0.15, G:0.32, T:0.19
Consensus pattern (98 bp):
AGATATGAAGGGAAAGGTTGAGGCGCAACGGCGAACCCGGTACCTTAGAAGATGTGATGGGAAGG
ATTGAGGCCGCAATGACGAATCTGGTACCATGA
Found at i:190018 original size:42 final size:40
Alignment explanation
Indices: 189969--190477 Score: 460
Period size: 42 Copynumber: 12.9 Consensus size: 40
189959 CAAAGACATG
* * * *
189969 CAATCTCTTGCCCCAATCATGGGGCAGATTAAAGACATTATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAG-C-TCATC
*
190011 CAATCTCTTACCCCGATCATAGGGCAGATTGAAGC-CATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCTCATC
* * *
190050 CAAT-TCTTACCCCGATCAAGGGGTAGATTGAAGACACCATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAG-C-TCATC
*
190091 CAATCTCTTACCCCGATCATGAGGCAGATTGAAG-TCATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCTCATC
190130 CAATCTCTTACCCCGATCAT------G---G--GC-CATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCTCATC
** *
190158 CAATCTCTTACATCGATCATGGGGCAGATTGAA-TTCATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCTCATC
* * *
190197 CAATCTCTCACCTCGATCATAGGGCAGATTGAAGACATCATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAG-C-TCATC
* * * * *
190239 TAATCTCTTACCCCGATCATGAGGTAGATTAAAGACATCATT
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAG-C-TCATC
* *
190281 CAATCTCTTACTCCGATCATGGGGCAGATTGAAG-TCATT
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCTCATC
* *
190320 CAATCTCTTACCCCGATCATTGGGTAGATTGAAGCT-ATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCTCATC
* * *
190359 CAATCTCCTACCCTGATCATGAGGCAGATTGAAGACATCATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAG-C-TCATC
* * * * *
190401 CAATCTTTTACGCTGATCATAGGGCAGATTAAAGACATCATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAG-C-TCATC
* * * *
190443 TAATCTCTTACCTCGATCATGAGGCAAATTGAAGC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGC
190478 ATTTAATCTT
Statistics
Matches: 387, Mismatches: 56, Indels: 49
0.79 0.11 0.10
Matches are distributed among these distances:
28 23 0.06
30 1 0.00
33 1 0.00
34 1 0.00
37 1 0.00
38 26 0.07
39 133 0.34
40 2 0.01
41 11 0.03
42 188 0.49
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (40 bp):
CAATCTCTTACCCCGATCATGGGGCAGATTGAAGCTCATC
Found at i:190094 original size:80 final size:81
Alignment explanation
Indices: 189969--190148 Score: 265
Period size: 80 Copynumber: 2.2 Consensus size: 81
189959 CAAAGACATG
* * * **
189969 CAATCTCTTGCCCCAATCATGGGGCAGATTAAAGACATTATCCAATCTCTTACCCCGATCAT-AG
1 CAATCTCTTACCCCGATCAAGGGGCAGATTAAAGACACCATCCAATCTCTTACCCCGATCATGA-
190033 GGCAGATTGAAGCCATC
65 GGCAGATTGAAGCCATC
* *
190050 CAAT-TCTTACCCCGATCAAGGGGTAGATTGAAGACACCATCCAATCTCTTACCCCGATCATGAG
1 CAATCTCTTACCCCGATCAAGGGGCAGATTAAAGACACCATCCAATCTCTTACCCCGATCATGAG
*
190114 GCAGATTGAAGTCATC
66 GCAGATTGAAGCCATC
190130 CAATCTCTTACCCCGATCA
1 CAATCTCTTACCCCGATCA
190149 TGGGCCATCC
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
80 70 0.79
81 19 0.21
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (81 bp):
CAATCTCTTACCCCGATCAAGGGGCAGATTAAAGACACCATCCAATCTCTTACCCCGATCATGAG
GCAGATTGAAGCCATC
Found at i:190166 original size:28 final size:28
Alignment explanation
Indices: 190126--190180 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
190116 AGATTGAAGT
*
190126 CATCCAATCTCTTACCCCGATCATGGGC
1 CATCCAATCTCTTACACCGATCATGGGC
*
190154 CATCCAATCTCTTACATCGATCATGGG
1 CATCCAATCTCTTACACCGATCATGGG
190181 GCAGATTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.27
Consensus pattern (28 bp):
CATCCAATCTCTTACACCGATCATGGGC
Found at i:190196 original size:67 final size:68
Alignment explanation
Indices: 190086--190221 Score: 211
Period size: 67 Copynumber: 2.0 Consensus size: 68
190076 ATTGAAGACA
* *
190086 CCATCCAATCTCTTACCCCGATCATGAGGCAGATTGAAGTCATCCAATCTCTTACCCCGATCAT-
1 CCATCCAATCTCTTACACCGATCATGAGGCAGATTGAAGTCATCCAATCTCTCACCCCGATCATA
190150 GGG
66 GGG
* * * *
190153 CCATCCAATCTCTTACATCGATCATGGGGCAGATTGAATTCATCCAATCTCTCACCTCGATCATA
1 CCATCCAATCTCTTACACCGATCATGAGGCAGATTGAAGTCATCCAATCTCTCACCCCGATCATA
190218 GGG
66 GGG
190221 C
1 C
190222 AGATTGAAGA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
67 58 0.94
68 4 0.06
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (68 bp):
CCATCCAATCTCTTACACCGATCATGAGGCAGATTGAAGTCATCCAATCTCTCACCCCGATCATA
GGG
Found at i:190432 original size:162 final size:161
Alignment explanation
Indices: 190158--190492 Score: 423
Period size: 162 Copynumber: 2.1 Consensus size: 161
190148 ATGGGCCATC
** *
190158 CAATCTCTTACATCGATCATGGGGCAGATTGAATTCATCCAATCTCTCACCTCGATCATAGGGCA
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAACTCATCCAATCTCTCACCTCGATCATAGGGCA
* *
190223 GATTGAAGACATCATCTAATCTCTTACCCCGATCATGAGGTAGATTAAAGACATCAT-TCAATCT
66 GATTGAAGACATCATCCAATCTCTTACCCCGATCATGAGGCAGATTAAAGACATCATCT-AATCT
* *
190287 CTTA-CTCCGATCATGGGGCAGATTGAAGTCATT
130 CTTACCT-CGATCATGAGGCAAATTGAAG-CATT
* *
190320 CAATCTCTTACCCCGATCATTGGGTAGATTGAAGCT-ATCCAATCTC-CTACC-CTGATCAT-GA
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAA-CTCATCCAATCTCTC-ACCTC-GATCATAG-
* * *
190381 GGCAGATTGAAGACATCATCCAATCTTTTACGCTGATCAT-AGGGCAGATTAAAGACATCATCTA
62 GGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGA-GGCAGATTAAAGACATCATCTA
190445 ATCTCTTACCTCGATCATGAGGCAAATTGAAGCATT
126 ATCTCTTACCTCGATCATGAGGCAAATTGAAGCATT
* *
190481 TAATCTTTTACC
1 CAATCTCTTACC
190493 TTAACTAAAA
Statistics
Matches: 152, Mismatches: 14, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
161 18 0.12
162 130 0.86
163 4 0.03
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (161 bp):
CAATCTCTTACCCCGATCATGGGGCAGATTGAACTCATCCAATCTCTCACCTCGATCATAGGGCA
GATTGAAGACATCATCCAATCTCTTACCCCGATCATGAGGCAGATTAAAGACATCATCTAATCTC
TTACCTCGATCATGAGGCAAATTGAAGCATT
Found at i:193508 original size:14 final size:14
Alignment explanation
Indices: 193471--193512 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
193461 TTATATTTTA
193471 AATATTTAAATA-T
1 AATATTTAAATATT
193484 AATCA-TTAAATATT
1 AAT-ATTTAAATATT
*
193498 TATATTTAAATATT
1 AATATTTAAATATT
193512 A
1 A
193513 GCACAGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATTTAAATATT
Found at i:195280 original size:72 final size:72
Alignment explanation
Indices: 195173--195428 Score: 424
Period size: 72 Copynumber: 3.6 Consensus size: 72
195163 AACAAATTTT
* * * *
195173 ATATCC-AAAATCAAATATAAACAGCTATTGATAAAACTAAATTACACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
195237 AAATTCA
66 AAATTCA
* *
195244 ATATCCAAAAACCAAACATAAACAACTACTGATAAAACTAGATTGCACATAAATAAGTAGAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
195309 AAATTCA
66 AAATTCA
* * *
195316 ATATCCAAAAATCAAACATAAACAATTATTGATAAAACTAGATTACACATAAATAAGTAAAACAT
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
195381 AAATTCA
66 AAATTCA
195388 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAG
1 ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAG
195429 TTTAGTATTG
Statistics
Matches: 171, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
71 6 0.04
72 165 0.96
ACGTcount: A:0.55, C:0.16, G:0.05, T:0.23
Consensus pattern (72 bp):
ATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACAT
AAATTCA
Found at i:195888 original size:18 final size:18
Alignment explanation
Indices: 195855--195924 Score: 97
Period size: 18 Copynumber: 3.9 Consensus size: 18
195845 CGTTTCCATC
*
195855 AATGTTAACTTCATTTGA
1 AATGTTAACATCATTTGA
195873 AAT-TTGAACATCATTTGA
1 AATGTT-AACATCATTTGA
* *
195891 AGTGTTAACATCATTTAA
1 AATGTTAACATCATTTGA
195909 AATGTTAACATCATTT
1 AATGTTAACATCATTT
195925 CCTGAATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
17 2 0.04
18 42 0.91
19 2 0.04
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.41
Consensus pattern (18 bp):
AATGTTAACATCATTTGA
Found at i:199831 original size:8 final size:8
Alignment explanation
Indices: 199818--199842 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
199808 AAACTTGCTA
199818 TGATTTTC
1 TGATTTTC
199826 TGATTTTC
1 TGATTTTC
199834 TGATTTTC
1 TGATTTTC
199842 T
1 T
199843 CTCGTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (8 bp):
TGATTTTC
Found at i:202840 original size:22 final size:22
Alignment explanation
Indices: 202813--202864 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
202803 CAAATGAACG
**
202813 GAGAGCACCGAGGTGCTAAACA
1 GAGAGCACAAAGGTGCTAAACA
* *
202835 GAGAGCACAAATGTGCTAAATA
1 GAGAGCACAAAGGTGCTAAACA
202857 GAGAGCAC
1 GAGAGCAC
202865 TTTACGTGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.19, G:0.29, T:0.12
Consensus pattern (22 bp):
GAGAGCACAAAGGTGCTAAACA
Found at i:202877 original size:23 final size:22
Alignment explanation
Indices: 202825--202931 Score: 70
Period size: 27 Copynumber: 4.4 Consensus size: 22
202815 GAGCACCGAG
* *
202825 GTGCTAAACAGAGAGCACAAAT
1 GTGCTAAATAGAGAGCACAAAC
**
202847 GTGCTAAATAGAGAGCACTTTAC
1 GTGCTAAATAGAGAGCAC-AAAC
202870 GTGCTAAATAATCGGAGAGCACAATAC
1 GTGCTAAAT-A---GAGAGCACAA-AC
*
202897 GTGCTAAAATAACGGAGAGCACACAAA
1 GTGCT-AAAT-A--GAGAGCACA-AAC
202924 GTGCTAAA
1 GTGCTAAA
202932 CGGTGAGCGT
Statistics
Matches: 70, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
22 17 0.24
23 10 0.14
24 1 0.01
26 3 0.04
27 32 0.46
28 7 0.10
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (22 bp):
GTGCTAAATAGAGAGCACAAAC
Found at i:202897 original size:27 final size:26
Alignment explanation
Indices: 202835--202919 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 26
202825 GTGCTAAACA
*
202835 GAGAGCACAA-ATGTGCTAAAT-A--
1 GAGAGCACAATACGTGCTAAATAACG
**
202857 GAGAGCACTTTACGTGCTAAATAATCG
1 GAGAGCACAATACGTGCTAAATAA-CG
202884 GAGAGCACAATACGTGCTAAAATAACG
1 GAGAGCACAATACGTGCT-AAATAACG
202911 GAGAGCACA
1 GAGAGCACA
202920 CAAAGTGCTA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
22 8 0.15
23 10 0.19
24 1 0.02
27 27 0.52
28 6 0.12
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.18
Consensus pattern (26 bp):
GAGAGCACAATACGTGCTAAATAACG
Found at i:202927 original size:27 final size:28
Alignment explanation
Indices: 202870--202931 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
202860 AGCACTTTAC
*
202870 GTGCT-AAATAATCGGAGAGCACAATAC
1 GTGCTAAAATAATCGGAGAGCACAATAA
202897 GTGCTAAAATAA-CGGAGAGCACACA-AA
1 GTGCTAAAATAATCGGAGAGCACA-ATAA
202924 GTGCTAAA
1 GTGCTAAA
202932 CGGTGAGCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 25 0.78
28 7 0.22
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.16
Consensus pattern (28 bp):
GTGCTAAAATAATCGGAGAGCACAATAA
Found at i:208592 original size:21 final size:21
Alignment explanation
Indices: 208567--208630 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
208557 AGTTATCTCA
208567 AATAATATAAAATATTATATT
1 AATAATATAAAATATTATATT
* * *
208588 AATAATATTAAAAGTAATAAATA
1 AATAATA-TAAAA-TATTATATT
208611 AATAAT-TAAAA-ATTAATATT
1 AATAATATAAAATATT-ATATT
208631 TATTTTCATC
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 12 0.35
22 5 0.15
23 12 0.35
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AATAATATAAAATATTATATT
Found at i:210555 original size:27 final size:27
Alignment explanation
Indices: 210525--210586 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
210515 CGTTCCAGGG
* * *
210525 TGGTCAGGCGATAG-GTATCATACGGGT
1 TGGTCAGGCGAT-GCATATAATACGAGT
*
210552 TGGTCAGGTGATGCATATAATACGAGT
1 TGGTCAGGCGATGCATATAATACGAGT
210579 TGGTCAGG
1 TGGTCAGG
210587 GCACGAGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.03
27 29 0.97
ACGTcount: A:0.24, C:0.13, G:0.35, T:0.27
Consensus pattern (27 bp):
TGGTCAGGCGATGCATATAATACGAGT
Found at i:211109 original size:21 final size:21
Alignment explanation
Indices: 211085--211125 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
211075 GGAGTTGTAA
* *
211085 TAAACCTTAAAATCTAAACTC
1 TAAACATTAAAACCTAAACTC
*
211106 TAAACATTAAACCCTAAACT
1 TAAACATTAAAACCTAAACT
211126 TATTTACGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (21 bp):
TAAACATTAAAACCTAAACTC
Found at i:211369 original size:26 final size:26
Alignment explanation
Indices: 211287--211370 Score: 96
Period size: 26 Copynumber: 3.2 Consensus size: 26
211277 CTAAACCATG
*
211287 AATACAAACATCAAAATAATTAATTA
1 AATACAAACATAAAAATAATTAATTA
* * * *
211313 AATACAAATATAAACATCATTAATCA
1 AATACAAACATAAAAATAATTAATTA
* *
211339 AATACAAACATAAAAATTATTCATTA
1 AATACAAACATAAAAATAATTAATTA
*
211365 CATACA
1 AATACA
211371 TATTATTTAT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.27
Consensus pattern (26 bp):
AATACAAACATAAAAATAATTAATTA
Found at i:212901 original size:25 final size:26
Alignment explanation
Indices: 212851--212921 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 26
212841 ACTCTTCTGT
* *
212851 TTCCTTTCTTTTTTAAAAAATTTTGC
1 TTCCTTTCCTTCTTAAAAAATTTTGC
*
212877 TTCCTTTCCTTCTTCAAAAA-TTTGC
1 TTCCTTTCCTTCTTAAAAAATTTTGC
*
212902 TTCTTTTCCTTCTTAAAAAA
1 TTCCTTTCCTTCTTAAAAAA
212922 ATTATCTTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
25 23 0.57
26 17 0.43
ACGTcount: A:0.24, C:0.21, G:0.03, T:0.52
Consensus pattern (26 bp):
TTCCTTTCCTTCTTAAAAAATTTTGC
Found at i:212922 original size:26 final size:26
Alignment explanation
Indices: 212863--212932 Score: 90
Period size: 25 Copynumber: 2.7 Consensus size: 26
212853 CCTTTCTTTT
* *
212863 TTAAAAAATTTTGCTTCCTTTCCTTC
1 TTAAAAAAATTTGCTTCTTTTCCTTC
*
212889 TT-CAAAAATTTGCTTCTTTTCCTTC
1 TTAAAAAAATTTGCTTCTTTTCCTTC
212914 TTAAAAAAATTAT-CTTCTT
1 TTAAAAAAATT-TGCTTCTT
212933 ACTCAATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 22 0.58
26 15 0.39
27 1 0.03
ACGTcount: A:0.27, C:0.20, G:0.03, T:0.50
Consensus pattern (26 bp):
TTAAAAAAATTTGCTTCTTTTCCTTC
Found at i:213029 original size:27 final size:27
Alignment explanation
Indices: 212999--213076 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
212989 GACAGCACTA
* **
212999 GTGCTACCTAACCAGTAGGCACCATTG
1 GTGCCACCTAACCAAAAGGCACCATTG
* *
213026 GTGCCGCCTATCCAAAAGGCACCATTG
1 GTGCCACCTAACCAAAAGGCACCATTG
* *
213053 GTGCCGCCTACCCAAAAGGCACCA
1 GTGCCACCTAACCAAAAGGCACCA
213077 CCCATCCGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.27, C:0.35, G:0.22, T:0.17
Consensus pattern (27 bp):
GTGCCACCTAACCAAAAGGCACCATTG
Found at i:215560 original size:6 final size:6
Alignment explanation
Indices: 215549--215633 Score: 90
Period size: 6 Copynumber: 15.0 Consensus size: 6
215539 AAAAAATTAT
* * *
215549 TTTAAA TTTAAA TTT-AT TTTAAG TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
215595 -TTAAT TTTAAA TTTGAA TTTAAA TTT--A TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
215634 ATAAATAAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
4 4 0.06
5 12 0.18
6 49 0.75
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:215567 original size:17 final size:17
Alignment explanation
Indices: 215545--215615 Score: 115
Period size: 17 Copynumber: 4.2 Consensus size: 17
215535 TCTTAAAAAA
215545 TTATTTTAAATTTAAAT
1 TTATTTTAAATTTAAAT
*
215562 TTATTTTAAGTTTAAAT
1 TTATTTTAAATTTAAAT
215579 TTATTTTAAATTTAAAT
1 TTATTTTAAATTTAAAT
* *
215596 TAATTTTAAATTTGAAT
1 TTATTTTAAATTTAAAT
215613 TTA
1 TTA
215616 AATTTATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 49 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTATTTTAAATTTAAAT
Found at i:215575 original size:11 final size:11
Alignment explanation
Indices: 215555--215631 Score: 59
Period size: 11 Copynumber: 6.9 Consensus size: 11
215545 TTATTTTAAA
215555 TTTAAATTTAT
1 TTTAAATTTAT
* *
215566 TTTAAGTTTAAA
1 TTTAAATTT-AT
* *
215578 TTT-ATTTTAAA
1 TTTAAATTT-AT
*
215589 TTTAAATTAAT
1 TTTAAATTTAT
*
215600 TTTAAATTTGAA
1 TTTAAATTT-AT
215612 TTTAAATTTA-
1 TTTAAATTTAT
215622 TTTAAATTTA
1 TTTAAATTTA
215632 AAATAAATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
10 10 0.18
11 28 0.51
12 17 0.31
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:215583 original size:34 final size:34
Alignment explanation
Indices: 215545--215631 Score: 115
Period size: 34 Copynumber: 2.6 Consensus size: 34
215535 TCTTAAAAAA
*
215545 TTATTTTAAATTTAAATTTATTTTAAGTTTAAAT
1 TTATTTTAAATTTAAATTTATTTTAAATTTAAAT
* *
215579 TTATTTTAAATTTAAATTAATTTTAAATTTGAAT
1 TTATTTTAAATTTAAATTTATTTTAAATTTAAAT
*
215613 TTAAATTT--ATTTAAATTTA
1 TT-ATTTTAAATTTAAATTTA
215632 AAATAAATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
33 10 0.21
34 33 0.70
35 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (34 bp):
TTATTTTAAATTTAAATTTATTTTAAATTTAAAT
Found at i:215590 original size:28 final size:28
Alignment explanation
Indices: 215553--215633 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
215543 AATTATTTTA
*
215553 AATTTAAATTTATTTTAAGTTTAAATTT-
1 AATTTAAATTTA-TTTAAATTTAAATTTG
* * *
215581 ATTTTAAATTTAAATTAATTTTAAATTTG
1 AATTTAAATTT-ATTTAAATTTAAATTTG
215610 AATTTAAATTTATTTAAATTTAAA
1 AATTTAAATTTATTTAAATTTAAA
215634 ATAAATAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 34 0.76
29 11 0.24
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
AATTTAAATTTATTTAAATTTAAATTTG
Found at i:215964 original size:22 final size:22
Alignment explanation
Indices: 215939--215992 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
215929 GCAAAGAAGG
*
215939 AAAAGACAAGCAATTAAGTTGT
1 AAAAGACAAACAATTAAGTTGT
215961 AAAAGACAAACAATTAAGTTGT
1 AAAAGACAAACAATTAAGTTGT
215983 AAAAGACAAA
1 AAAAGACAAA
215993 ATAAAATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.57, C:0.09, G:0.15, T:0.19
Consensus pattern (22 bp):
AAAAGACAAACAATTAAGTTGT
Found at i:217481 original size:29 final size:29
Alignment explanation
Indices: 217430--217791 Score: 260
Period size: 29 Copynumber: 12.6 Consensus size: 29
217420 CCCTACACTT
* *
217430 TTCC-AAAATTACA-TTTTGCCTCTGAAC
1 TTCCAAAAATTACATTTTTACCTCTAAAC
* *
217457 TTCTAAAAATTACATCTTTACCTCTAAAC
1 TTCCAAAAATTACATTTTTACCTCTAAAC
** *
217486 TTCCAAAAATTATGTTTTTGTCC-CTAAAC
1 TTCCAAAAATTACATTTTT-ACCTCTAAAC
* * *
217515 TTCTAAAAAATTACATTTTTCCCTC-GAAC
1 TTC-CAAAAATTACATTTTTACCTCTAAAC
* *
217544 TTCCAAAAATTACATTTGT--CACTAAAC
1 TTCCAAAAATTACATTTTTACCTCTAAAC
* *
217571 TTTCAAAAATTACATTTTTGCC-CTAAAC
1 TTCCAAAAATTACATTTTTACCTCTAAAC
* * *
217599 TTCTCAAAAATCACATTTTTACCCCCAAAC
1 TTC-CAAAAATTACATTTTTACCTCTAAAC
* ** *
217629 TTCCAAAAATTATATTTTGCCCTC-GAAC
1 TTCCAAAAATTACATTTTTACCTCTAAAC
* *
217657 TTCCAAAAATTGCATTTTTACCATCTGAAC
1 TTCCAAAAATTACATTTTTACC-TCTAAAC
* * **
217687 TTCC-AAAATTACATTTTTTCCCCCGAAC
1 TTCCAAAAATTACATTTTTACCTCTAAAC
* ** * * **
217715 TTCCAAAAATAATGTTTTTACCCCGAATT
1 TTCCAAAAATTACATTTTTACCTCTAAAC
* *
217744 TTCTC-AAAATAACATTTTTACCCCTAAAAC
1 TTC-CAAAAATTACATTTTTACCTCT-AAAC
217774 TTTCC-AAAATTACATTTT
1 -TTCCAAAAATTACATTTT
217792 AACCCCAAAT
Statistics
Matches: 267, Mismatches: 52, Indels: 29
0.77 0.15 0.08
Matches are distributed among these distances:
26 2 0.01
27 23 0.09
28 61 0.23
29 130 0.49
30 48 0.18
31 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.37
Consensus pattern (29 bp):
TTCCAAAAATTACATTTTTACCTCTAAAC
Found at i:217695 original size:86 final size:84
Alignment explanation
Indices: 217395--217724 Score: 299
Period size: 87 Copynumber: 3.8 Consensus size: 84
217385 AAGGTCCCTG
* * * * * * * * *
217395 AACTATCCAAAAATAATATTTTGACCCCTACACTTTTCCAAAATTACATTTTGCCTCTGAACTTC
1 AACT-TCCAAAAATTACATTTTTA-CCCTAAACTTCTCAAAAATTACATTTTTCCCCCGAACTTC
* *
217460 TAAAAATTACATCTT-TACCTCTA
64 CAAAAATTACAT-TTGT--CACTA
** * * *
217483 AACTTCCAAAAATTATGTTTTTGTCCCTAAACTTCTAAAAAATTACATTTTTCCCTCGAACTTCC
1 AACTTCCAAAAATTACATTTTT-ACCCTAAACTTCTCAAAAATTACATTTTTCCCCCGAACTTCC
217548 AAAAATTACATTTGTCACTA
65 AAAAATTACATTTGTCACTA
* * * *
217568 AACTTTCAAAAATTACATTTTTGCCCTAAACTTCTCAAAAATCACATTTTTACCCCCAAACTTCC
1 AACTTCCAAAAATTACATTTTTACCCTAAACTTCTCAAAAATTACATTTTT-CCCCCGAACTTCC
* * *
217633 AAAAATTATATTT-TGCCCTCG
65 AAAAATTACATTTGT-CACT-A
* *
217654 AACTTCCAAAAATTGCATTTTTACCATCTGAACTTC-C-AAAATTACATTTTTTCCCCCGAACTT
1 AACTTCCAAAAATTACATTTTTACC--CTAAACTTCTCAAAAATTACA-TTTTTCCCCCGAACTT
217717 CCAAAAAT
63 CCAAAAAT
217725 AATGTTTTTA
Statistics
Matches: 203, Mismatches: 31, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
84 27 0.13
85 49 0.24
86 50 0.25
87 65 0.32
88 12 0.06
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (84 bp):
AACTTCCAAAAATTACATTTTTACCCTAAACTTCTCAAAAATTACATTTTTCCCCCGAACTTCCA
AAAATTACATTTGTCACTA
Found at i:217715 original size:28 final size:28
Alignment explanation
Indices: 217521--217791 Score: 158
Period size: 28 Copynumber: 9.5 Consensus size: 28
217511 AAACTTCTAA
*
217521 AAAATTACA-TTTTTCCCTCGAACTTCC
1 AAAATTACATTTTTTCCCCCGAACTTCC
* * ** *
217548 AAAAATTACA-TTTGT-CACTAAACTTTCA
1 -AAAATTACATTTTTTCCCCCGAAC-TTCC
* **
217576 AAAATTACA-TTTTTGCCCTAAACTTCTC
1 AAAATTACATTTTTTCCCCCGAACTTC-C
* * *
217604 AAAAATCACATTTTTACCCCCAAACTTCC
1 -AAAATTACATTTTTTCCCCCGAACTTCC
* * *
217633 AAAAATTATA-TTTTGCCCTCGAACTTCC
1 -AAAATTACATTTTTTCCCCCGAACTTCC
* * * *
217661 AAAAATTGCATTTTTACCATCTGAACTTCC
1 -AAAATTACATTTTTTCC-CCCGAACTTCC
217691 AAAATTACATTTTTTCCCCCGAACTTCC
1 AAAATTACATTTTTTCCCCCGAACTTCC
* * *
217719 AAAAATA-ATGTTTTTACCCCGAATTTTCTC
1 AAAATTACAT-TTTTTCCCCCGAA-CTTC-C
* * **
217749 AAAATAACATTTTTACCCCTAAAACTTTCC
1 AAAATTACATTTTTTCCCC-CGAAC-TTCC
217779 AAAATTACATTTT
1 AAAATTACATTTT
217792 AACCCCAAAT
Statistics
Matches: 191, Mismatches: 39, Indels: 24
0.75 0.15 0.09
Matches are distributed among these distances:
27 22 0.12
28 73 0.38
29 41 0.21
30 48 0.25
31 7 0.04
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (28 bp):
AAAATTACATTTTTTCCCCCGAACTTCC
Found at i:224765 original size:71 final size:71
Alignment explanation
Indices: 224684--224826 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
224674 ATGGGGACAA
224684 TGAAGGGTTTGAGCAACAATGCTGTATCAGAGGAAGGAAATGAAGGAAGAAACTCACGGGAGATT
1 TGAAGGGTTTGAGCAACAATGCTGTATCAGAGGAAGGAAATGAAGGAAGAAACTCACGGGAGATT
224749 CGTCCT
66 CGTCCT
224755 TGAAGGGTTTGAGCAACAATGCTGTATCAGAGGAAGGAAATGAAGGAAGAAACTCACGGGAGATT
1 TGAAGGGTTTGAGCAACAATGCTGTATCAGAGGAAGGAAATGAAGGAAGAAACTCACGGGAGATT
224820 CGTCCT
66 CGTCCT
224826 T
1 T
224827 TCGCCCCTAG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.35, C:0.14, G:0.31, T:0.20
Consensus pattern (71 bp):
TGAAGGGTTTGAGCAACAATGCTGTATCAGAGGAAGGAAATGAAGGAAGAAACTCACGGGAGATT
CGTCCT
Found at i:227366 original size:10 final size:10
Alignment explanation
Indices: 227351--227376 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
227341 AACCCATTCA
227351 AATGAGTATC
1 AATGAGTATC
227361 AATGAGTATC
1 AATGAGTATC
227371 AATGAG
1 AATGAG
227377 GCTCCGACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (10 bp):
AATGAGTATC
Found at i:228939 original size:17 final size:19
Alignment explanation
Indices: 228917--228952 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
228907 TGATCGTTTT
228917 GAATATA-TTAATA-ATAG
1 GAATATATTTAATACATAG
228934 GAATATATTTAATACATAG
1 GAATATATTTAATACATAG
228953 TTATTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 6 0.35
19 4 0.24
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.36
Consensus pattern (19 bp):
GAATATATTTAATACATAG
Found at i:229121 original size:15 final size:14
Alignment explanation
Indices: 229095--229158 Score: 60
Period size: 15 Copynumber: 4.5 Consensus size: 14
229085 AAAAAATTGA
229095 TAAAT-TAAAAAAT
1 TAAATGTAAAAAAT
229108 TAAATGCTACAAAAA-
1 TAAATG-TA-AAAAAT
**
229123 TAAATGTTGAAAAT
1 TAAATGTAAAAAAT
*
229137 TAAATATTAAAAAAT
1 TAAAT-GTAAAAAAT
229152 TAAATGT
1 TAAATGT
229159 TTTATTCAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
13 9 0.22
14 7 0.17
15 19 0.47
16 5 0.12
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.31
Consensus pattern (14 bp):
TAAATGTAAAAAAT
Found at i:229141 original size:29 final size:29
Alignment explanation
Indices: 229103--229159 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
229093 GATAAATTAA
*
229103 AAAATTAAATGCTACAAAAA-TAAATGTTG
1 AAAATTAAATACTA-AAAAATTAAATGTTG
*
229132 AAAATTAAATATTAAAAAATTAAATGTT
1 AAAATTAAATACTAAAAAATTAAATGTT
229160 TTATTCAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.32
Consensus pattern (29 bp):
AAAATTAAATACTAAAAAATTAAATGTTG
Found at i:229643 original size:230 final size:230
Alignment explanation
Indices: 229240--229654 Score: 688
Period size: 230 Copynumber: 1.8 Consensus size: 230
229230 TAAAAAAATA
* * *
229240 ATATAATCTTAAGTGAAATAGATAAAATAGAAGTGAATTGACTTTGGTAGTTCTTTATATATTAG
1 ATATAATCCTAAGTGAAATAGATAAAATAAAAGTGAATTGAATTTGGTAGTTCTTTATATATTAG
229305 ATAAATAGATAATCCAATTAACATGGTTTTATGTACCTTTATCCATTTTTTAGTGAATTATAAAG
66 ATAAATAGATAATCCAATTAACATGGTTTTATGTACCTTTATCCATTTTTTAGTGAATTATAAAG
* *
229370 GAAGGGCAAAGCCCTAACAATGAAGCAATTGACGGGACTCGAACTCAAATCACATCTAGGACAAT
131 GAAGGGCAAAACCCTAAAAATGAAGCAATTGACGGGACTCGAACTCAAATCACATCTAGGACAAT
229435 GAATATCTTTAATCATTAGGCCAATACACGAGTTC
196 GAATATCTTTAATCATTAGGCCAATACACGAGTTC
*
229470 ATATAATCCTAAGTGAAATAGATAAAATAAAAGTGAATTGAATTTGGTATTTCTTTATATATTAG
1 ATATAATCCTAAGTGAAATAGATAAAATAAAAGTGAATTGAATTTGGTAGTTCTTTATATATTAG
* * *
229535 TTAAATAGATAATCTAATTAACATGGTTTTATGTACCTTTATCCATTTTTTGGTGAATTATAAAG
66 ATAAATAGATAATCCAATTAACATGGTTTTATGTACCTTTATCCATTTTTTAGTGAATTATAAAG
* * ** *
229600 GGAGGGTAAAACTTTAAAAAT-AACGCGATTGACGGGACTCGAACTCAAATCACAT
131 GAAGGGCAAAACCCTAAAAATGAA-GCAATTGACGGGACTCGAACTCAAATCACAT
229655 AGGAGGCAAT
Statistics
Matches: 170, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
229 2 0.01
230 168 0.99
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (230 bp):
ATATAATCCTAAGTGAAATAGATAAAATAAAAGTGAATTGAATTTGGTAGTTCTTTATATATTAG
ATAAATAGATAATCCAATTAACATGGTTTTATGTACCTTTATCCATTTTTTAGTGAATTATAAAG
GAAGGGCAAAACCCTAAAAATGAAGCAATTGACGGGACTCGAACTCAAATCACATCTAGGACAAT
GAATATCTTTAATCATTAGGCCAATACACGAGTTC
Found at i:240370 original size:14 final size:14
Alignment explanation
Indices: 240351--240401 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
240341 TTTAAAAAAT
240351 TCAACGGGTCAA-GA
1 TCAAC-GGTCAACGA
240365 TCAACGGTCAACGA
1 TCAACGGTCAACGA
* * *
240379 TCAATGATCAACAA
1 TCAACGGTCAACGA
240393 TCAACGGTC
1 TCAACGGTC
240402 GGTCAATGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
13 6 0.19
14 25 0.81
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (14 bp):
TCAACGGTCAACGA
Found at i:240377 original size:21 final size:22
Alignment explanation
Indices: 240351--240399 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
240341 TTTAAAAAAT
* **
240351 TCAACGGGTCAA-GATCAACGG
1 TCAACGGATCAATGATCAACAA
240372 TCAAC-GATCAATGATCAACAA
1 TCAACGGATCAATGATCAACAA
240393 TCAACGG
1 TCAACGG
240400 TCGGTCAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.22
21 17 0.74
22 1 0.04
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.16
Consensus pattern (22 bp):
TCAACGGATCAATGATCAACAA
Found at i:247800 original size:24 final size:24
Alignment explanation
Indices: 247371--247816 Score: 281
Period size: 24 Copynumber: 18.6 Consensus size: 24
247361 ATCTGAATAA
* **
247371 CTGACAAGCGTAAACGTACAGAAG
1 CTGACGAGCGTAAACGTACATTAG
* * **
247395 TTGACGAGCATAAACGTACAGAAG
1 CTGACGAGCGTAAACGTACATTAG
* * **
247419 TTGACGAGCGTAAATGTACAGAAG
1 CTGACGAGCGTAAACGTACATTAG
* * *
247443 CTGACAAGCGTAAAAGTACAGTA-
1 CTGACGAGCGTAAACGTACATTAG
* **
247466 TTCGACGAGCGTAAACGTACAAAAG
1 CT-GACGAGCGTAAACGTACATTAG
**
247491 CT-ATCGAGCGTAAACAG-ACAGAAG
1 CTGA-CGAGCGTAAAC-GTACATTAG
* * **
247515 ATGACGAGCATAAACGTACAAAAG
1 CTGACGAGCGTAAACGTACATTAG
* * * **
247539 CTAACGAGTGTAAACGTATAGAAG
1 CTGACGAGCGTAAACGTACATTAG
* * *
247563 CTAACGAGCATAAACGAACATT-G
1 CTGACGAGCGTAAACGTACATTAG
* * **
247586 -TTACCGAGCGTAAACGTATAAAAG
1 CTGA-CGAGCGTAAACGTACATTAG
** * * *
247610 CTGAAAAGCATAAACGTACAATAA
1 CTGACGAGCGTAAACGTACATTAG
* * **
247634 CTGACAAGCATAAACGTATGTTAG
1 CTGACGAGCGTAAACGTACATTAG
* * *
247658 CTGACAAGCGTAAATGTATATTAG
1 CTGACGAGCGTAAACGTACATTAG
*
247682 CTGACGAGCGTAAACGTATATTAG
1 CTGACGAGCGTAAACGTACATTAG
* * *
247706 CTGACGAGCATGAACGTATATTAG
1 CTGACGAGCGTAAACGTACATTAG
* * *
247730 TTGGCGAGCGTAAACGTACAATAG
1 CTGACGAGCGTAAACGTACATTAG
* *
247754 CTGACAAGCATAAACGTACATTAG
1 CTGACGAGCGTAAACGTACATTAG
*
247778 CTGACGAGCGTAAACGTATATTAG
1 CTGACGAGCGTAAACGTACATTAG
* * *
247802 TTGATGAACGTAAAC
1 CTGACGAGCGTAAAC
247817 ATAATGAAAT
Statistics
Matches: 340, Mismatches: 73, Indels: 18
0.79 0.17 0.04
Matches are distributed among these distances:
22 2 0.01
23 17 0.05
24 316 0.93
25 5 0.01
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (24 bp):
CTGACGAGCGTAAACGTACATTAG
Found at i:247802 original size:72 final size:72
Alignment explanation
Indices: 247372--247816 Score: 310
Period size: 72 Copynumber: 6.2 Consensus size: 72
247362 TCTGAATAAC
* * * * * *
247372 TGACAAGCGTAAACGTACAGA-AGTTGACGAGCATAAACGTACAGAAGTTGACGAGCGTAAATGT
1 TGACGAGCGTAAACGTACA-ATAGCTGACGAGCATAAACGTACAAAAGCTGACGAGCATAAACGT
** *
247436 ACAGAAGC
65 ACATTAGT
* * * * * *
247444 TGACAAGCGTAAAAGTACAGTA-TTCGACGAGCGTAAACGTACAAAAGCT-ATCGAGCGTAAACA
1 TGACGAGCGTAAACGTACAATAGCT-GACGAGCATAAACGTACAAAAGCTGA-CGAGCATAAAC-
** *
247507 G-ACAGAAGA
63 GTACATTAGT
* * * ** * * * *
247516 TGACGAGCATAAACGTACAAAAGCTAACGAGTGTAAACGTATAGAAGCTAACGAGCATAAACGAA
1 TGACGAGCGTAAACGTACAATAGCTGACGAGCATAAACGTACAAAAGCTGACGAGCATAAACGTA
247581 CATT-GT
66 CATTAGT
* * ** *
247587 T-ACCGAGCGTAAACGTATAAAAGCTGAAAAGCATAAACGTACAATAA-CTGACAAGCATAAACG
1 TGA-CGAGCGTAAACGTACAATAGCTGACGAGCATAAACGTACAA-AAGCTGACGAGCATAAACG
** *
247650 TATGTTAGC
64 TACATTAGT
* * * * * * ** *
247659 TGACAAGCGTAAATGTATATTAGCTGACGAGCGTAAACGTATATTAGCTGACGAGCATGAACGTA
1 TGACGAGCGTAAACGTACAATAGCTGACGAGCATAAACGTACAAAAGCTGACGAGCATAAACGTA
*
247724 TATTAGT
66 CATTAGT
* * ** *
247731 TGGCGAGCGTAAACGTACAATAGCTGACAAGCATAAACGTACATTAGCTGACGAGCGTAAACGTA
1 TGACGAGCGTAAACGTACAATAGCTGACGAGCATAAACGTACAAAAGCTGACGAGCATAAACGTA
*
247796 TATTAGT
66 CATTAGT
* *
247803 TGATGAACGTAAAC
1 TGACGAGCGTAAAC
247817 ATAATGAAAT
Statistics
Matches: 298, Mismatches: 63, Indels: 24
0.77 0.16 0.06
Matches are distributed among these distances:
70 1 0.00
71 56 0.19
72 237 0.80
73 4 0.01
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (72 bp):
TGACGAGCGTAAACGTACAATAGCTGACGAGCATAAACGTACAAAAGCTGACGAGCATAAACGTA
CATTAGT
Found at i:254146 original size:30 final size:30
Alignment explanation
Indices: 254110--254208 Score: 120
Period size: 30 Copynumber: 3.4 Consensus size: 30
254100 TAGATGATTG
254110 AATTATCATTTTTCAACTACATTAATGACT
1 AATTATCATTTTTCAACTACATTAATGACT
* *
254140 AATTATCATTTTTTGAA--A-GTT-A--ACT
1 AATTATCA-TTTTTCAACTACATTAATGACT
254165 GAATTATCATTTTTCAACTACATTAATGACT
1 -AATTATCATTTTTCAACTACATTAATGACT
254196 AATTATCATTTTT
1 AATTATCATTTTT
254209 TGAAAGTTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
25 10 0.18
26 8 0.14
27 2 0.04
28 4 0.07
29 2 0.04
30 21 0.37
31 10 0.18
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.46
Consensus pattern (30 bp):
AATTATCATTTTTCAACTACATTAATGACT
Found at i:254169 original size:26 final size:26
Alignment explanation
Indices: 254140--254222 Score: 80
Period size: 26 Copynumber: 3.0 Consensus size: 26
254130 ATTAATGACT
254140 AATTATCATTTTTTGAAAGTTAACTG
1 AATTATCATTTTTTGAAAGTTAACTG
* *
254166 AATTATCA-TTTTTCAACTACATTAA-TG
1 AATTATCATTTTTTGAA--A-GTTAACTG
254193 ACTAATTATCATTTTTTGAAAGTTAACTG
1 ---AATTATCATTTTTTGAAAGTTAACTG
254222 A
1 A
254223 TTGAATTGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
25 7 0.16
26 9 0.20
27 3 0.07
28 8 0.18
29 3 0.07
30 8 0.18
31 7 0.16
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (26 bp):
AATTATCATTTTTTGAAAGTTAACTG
Found at i:254194 original size:56 final size:56
Alignment explanation
Indices: 254108--254222 Score: 230
Period size: 56 Copynumber: 2.1 Consensus size: 56
254098 AATAGATGAT
254108 TGAATTATCATTTTTCAACTACATTAATGACTAATTATCATTTTTTGAAAGTTAAC
1 TGAATTATCATTTTTCAACTACATTAATGACTAATTATCATTTTTTGAAAGTTAAC
254164 TGAATTATCATTTTTCAACTACATTAATGACTAATTATCATTTTTTGAAAGTTAAC
1 TGAATTATCATTTTTCAACTACATTAATGACTAATTATCATTTTTTGAAAGTTAAC
254220 TGA
1 TGA
254223 TTGAATTGAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (56 bp):
TGAATTATCATTTTTCAACTACATTAATGACTAATTATCATTTTTTGAAAGTTAAC
Found at i:257285 original size:28 final size:28
Alignment explanation
Indices: 257237--257299 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
257227 AAAATGAGAC
257237 TTTTCGGATACTCGGGAGTAAAATGGTAA
1 TTTT-GGATACTCGGGAGTAAAATGGTAA
* *
257266 TTTTGGATTCTCGAGG-GTAATATGGTAA
1 TTTTGGATACTCG-GGAGTAAAATGGTAA
257294 TTTTGG
1 TTTTGG
257300 GAAATTTAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 25 0.81
29 6 0.19
ACGTcount: A:0.25, C:0.08, G:0.29, T:0.38
Consensus pattern (28 bp):
TTTTGGATACTCGGGAGTAAAATGGTAA
Found at i:257435 original size:30 final size:30
Alignment explanation
Indices: 257399--257457 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
257389 ATTCGAGGGC
257399 AAAATGAAATTTTTTG-AAGTTTCGGGGTTA
1 AAAATGAAA-TTTTTGAAAGTTTCGGGGTTA
257429 AAAATGAAATTTTTGAAAGTTTCGGGGTT
1 AAAATGAAATTTTTGAAAGTTTCGGGGTT
257458 TTGGGGTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.39
Consensus pattern (30 bp):
AAAATGAAATTTTTGAAAGTTTCGGGGTTA
Found at i:257464 original size:38 final size:37
Alignment explanation
Indices: 257417--257491 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 37
257407 ATTTTTTGAA
*
257417 GTTTCGGGGTTAAAAATGAAATTTTTGAAAGTTTCGGG
1 GTTTCGGGGTCAAAAATGAAATTTTTGAAAG-TTCGGG
* * *
257455 GTTTTGGGGTCAAGAATGAAATTTTTGGAAGTTCGGG
1 GTTTCGGGGTCAAAAATGAAATTTTTGAAAGTTCGGG
257492 AGTAAAAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
37 6 0.18
38 27 0.82
ACGTcount: A:0.27, C:0.05, G:0.32, T:0.36
Consensus pattern (37 bp):
GTTTCGGGGTCAAAAATGAAATTTTTGAAAGTTCGGG
Done.