Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 98 of 171
Found at i:31858414 original size:61 final size:62
Alignment explanation
Indices: 31858341--31858467 Score: 211
Period size: 62 Copynumber: 2.1 Consensus size: 62
31858331 TATCCGTTGA
* * *
31858341 TAATAAAATCGAA-TTCTTTTGAATATTTTTGTACACATTAGTTTTGGCATATTGTTTTATT
1 TAATAAAATCGAAGTTCATTTGAATATTTTTGAACACATTAGTTTTGGCATATTGTTTCATT
*
31858402 TAATAAATTCGAAGTTCATTTGAATATTTTTGAACACATTAGTTTTGGCATATTGTTTCATT
1 TAATAAAATCGAAGTTCATTTGAATATTTTTGAACACATTAGTTTTGGCATATTGTTTCATT
31858464 TAAT
1 TAAT
31858468 TGAGAACCAA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
61 12 0.20
62 49 0.80
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.49
Consensus pattern (62 bp):
TAATAAAATCGAAGTTCATTTGAATATTTTTGAACACATTAGTTTTGGCATATTGTTTCATT
Found at i:31861824 original size:28 final size:28
Alignment explanation
Indices: 31861793--31861878 Score: 73
Period size: 28 Copynumber: 3.0 Consensus size: 28
31861783 TTAAAAAATT
31861793 CATCTTGTCAAAATAATTTTTCAAAACA
1 CATCTTGTCAAAATAATTTTTCAAAACA
** ** * * *
31861821 CATCACGTCAATTTCATTTTTCAGAACC
1 CATCTTGTCAAAATAATTTTTCAAAACA
* *
31861849 CATCTTCTCAAAATTATTTTTTCCAAAACA
1 CATCTTGTCAAAA-TAATTTTT-CAAAACA
31861879 ATTCCATATT
Statistics
Matches: 40, Mismatches: 16, Indels: 2
0.69 0.28 0.03
Matches are distributed among these distances:
28 29 0.73
29 6 0.15
30 5 0.12
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.37
Consensus pattern (28 bp):
CATCTTGTCAAAATAATTTTTCAAAACA
Found at i:31862036 original size:20 final size:21
Alignment explanation
Indices: 31861974--31862037 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
31861964 TAGCCCTTAA
* *
31861974 TTTAAAATACCAAAAGCCTAAT
1 TTTAAAAT-CCTAAACCCTAAT
31861996 TTTAAAATCCTAAACCCTAAT
1 TTTAAAATCCTAAACCCTAAT
31862017 TTTAAAATCCTAAA-CCTAAT
1 TTTAAAATCCTAAACCCTAAT
31862037 T
1 T
31862038 AAAATAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.17
21 25 0.62
22 8 0.20
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.33
Consensus pattern (21 bp):
TTTAAAATCCTAAACCCTAAT
Found at i:31862849 original size:11 final size:11
Alignment explanation
Indices: 31862833--31862857 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31862823 CATAACTCTC
31862833 TTTTTTTTCTT
1 TTTTTTTTCTT
31862844 TTTTTTTTCTT
1 TTTTTTTTCTT
31862855 TTT
1 TTT
31862858 GAGTCCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:31865329 original size:24 final size:22
Alignment explanation
Indices: 31865271--31865329 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
31865261 TATCCATACT
* *
31865271 AATAAATAATCATTTATTTAAA
1 AATAATTAATTATTTATTTAAA
*
31865293 AACAATTTAAATTATTTATTTCAAA
1 AATAA-TT-AATTATTTATTT-AAA
31865318 AGATAATTAATT
1 A-ATAATTAATT
31865330 TTAATAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
22 4 0.14
23 1 0.03
24 15 0.52
25 6 0.21
26 3 0.10
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (22 bp):
AATAATTAATTATTTATTTAAA
Found at i:31867380 original size:29 final size:30
Alignment explanation
Indices: 31867345--31867401 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
31867335 GTTTTCCGAA
**
31867345 TTTATTTTCTT-AATGTTGTGAGTTCAGAT
1 TTTATTTTCTTGAATAATGTGAGTTCAGAT
*
31867374 TTTATTTTTTTGAATAATGTGAGTTCAG
1 TTTATTTTCTTGAATAATGTGAGTTCAG
31867402 TATATTGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.23, C:0.05, G:0.18, T:0.54
Consensus pattern (30 bp):
TTTATTTTCTTGAATAATGTGAGTTCAGAT
Found at i:31874528 original size:32 final size:35
Alignment explanation
Indices: 31874492--31874571 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 35
31874482 GTGAAACAAT
*
31874492 AGAAATAAATAATTTT-AAATCACAAAAT-AAA-A
1 AGAAATAAATAATTTTAAAATCAAAAAATAAAATA
31874524 AGAAATAAATAATTTTAAAAATCAAAAAATAAAATA
1 AGAAATAAATAATTTT-AAAATCAAAAAATAAAATA
31874560 AGAAAATAAATA
1 AG-AAATAAATA
31874572 TAAATTTGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
32 16 0.38
34 11 0.26
35 3 0.07
36 3 0.07
37 9 0.21
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.24
Consensus pattern (35 bp):
AGAAATAAATAATTTTAAAATCAAAAAATAAAATA
Found at i:31880147 original size:26 final size:25
Alignment explanation
Indices: 31880098--31880197 Score: 87
Period size: 26 Copynumber: 3.9 Consensus size: 25
31880088 TAAACAAATG
* *
31880098 AATAGTAGGCCTT-GAGCCAGTGATT
1 AATAGCAGG-CTTCGAGCCGGTGATT
*
31880123 AATTAGCAAGCTTCGAGCCGGTGATT
1 AA-TAGCAGGCTTCGAGCCGGTGATT
* * *
31880149 GAATAGCAGGTTTTGAGCAGGTGATT
1 -AATAGCAGGCTTCGAGCCGGTGATT
31880175 AAATAGCAGGCTTC-ATGCCGGTG
1 -AATAGCAGGCTTCGA-GCCGGTG
31880198 TATAGTTGAC
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
25 6 0.10
26 52 0.87
27 2 0.03
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (25 bp):
AATAGCAGGCTTCGAGCCGGTGATT
Found at i:31883317 original size:19 final size:19
Alignment explanation
Indices: 31883293--31883335 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
31883283 AATTTAAAAC
31883293 CAACCTAACACCCTAACAA
1 CAACCTAACACCCTAACAA
31883312 CAACCTAACACCCTAACAA
1 CAACCTAACACCCTAACAA
31883331 CAACC
1 CAACC
31883336 AAAACCCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.44, G:0.00, T:0.09
Consensus pattern (19 bp):
CAACCTAACACCCTAACAA
Found at i:31886188 original size:31 final size:30
Alignment explanation
Indices: 31886147--31886216 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
31886137 AAGCCAAGAG
* * *
31886147 GACTGCTTTGTTAC-TTTTCGATAACTTTAGT
1 GACTGTTTTGTCACATTTTC-A-AACTTGAGT
*
31886178 GACTGTTTTGTCACATTTTCAAAGTTGAGT
1 GACTGTTTTGTCACATTTTCAAACTTGAGT
31886208 GACTGTTTT
1 GACTGTTTT
31886217 ATTAAATGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 16 0.47
31 13 0.38
32 5 0.15
ACGTcount: A:0.20, C:0.14, G:0.19, T:0.47
Consensus pattern (30 bp):
GACTGTTTTGTCACATTTTCAAACTTGAGT
Found at i:31895590 original size:155 final size:154
Alignment explanation
Indices: 31895394--31895722 Score: 346
Period size: 156 Copynumber: 2.1 Consensus size: 154
31895384 TAAAAGGTGA
* **** * * *
31895394 GAAGTAAAAGTTTAGAGAAAAATAAAAAGTTTTGTGGGTTTTCGAGGAGTAAAATTTT-GGGAGA
1 GAAGTAAAAGTTTTG-GAAAAATAAAAAGTTTTAAAAGTTTTCGAAGAATAAAATTTTAAGGA-A
* * ** *
31895458 GAGTAAAT-GGGGTAGTAAAATTTTGGAGGGAAAATATT-AAAAAAAAATTTAAGGGGGGATGTG
64 -AGTAAATAAGGG-AGTAAAATTTTGAAGGGAAAATATTCAAAAAAAAA-TTAAGGGGAAATGGG
* *
31895521 TTTGGGGTAGATGTG-GGGTGGGAT-AGAAGG
126 TTTGAGGTAGATG-GAGAGTGGGATGAG-A-G
*
31895551 GAAGTAAAAGTTTTGGAAAAA-AAAAAGTTTTAAAAGTTTTTGAAGAATAAAATTTTCAAGGAAA
1 GAAGTAAAAGTTTTGGAAAAATAAAAAGTTTTAAAAGTTTTCGAAGAATAAAATTTT-AAGGAAA
* * *
31895615 GTAAATCAATGGAGTAAAATTTTGAAGGGAAAATATTCAAAAGAAAATTGAGGGGAAATGGGTTT
65 GTAAAT-AAGGGAGTAAAATTTTGAAGGGAAAATATTCAAAAAAAAATTAAGGGGAAATGGGTTT
31895680 GAGGTAGATGGAGAGTGGGATGAGAG
129 GAGGTAGATGGAGAGTGGGATGAGAG
31895706 GAGAGTAAAAGTTTTGG
1 GA-AGTAAAAGTTTTGG
31895723 GGGGAAAGTG
Statistics
Matches: 145, Mismatches: 19, Indels: 17
0.80 0.10 0.09
Matches are distributed among these distances:
155 39 0.27
156 77 0.53
157 29 0.20
ACGTcount: A:0.41, C:0.01, G:0.31, T:0.27
Consensus pattern (154 bp):
GAAGTAAAAGTTTTGGAAAAATAAAAAGTTTTAAAAGTTTTCGAAGAATAAAATTTTAAGGAAAG
TAAATAAGGGAGTAAAATTTTGAAGGGAAAATATTCAAAAAAAAATTAAGGGGAAATGGGTTTGA
GGTAGATGGAGAGTGGGATGAGAG
Found at i:31895602 original size:26 final size:25
Alignment explanation
Indices: 31895555--31895606 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
31895545 AGAAGGGAAG
31895555 TAAAAGTTTTGGAAAAAAAAAAGTTT
1 TAAAAGTTTTGGAAAAAAAAAA-TTT
* * *
31895581 TAAAAGTTTTTGAAGAATAAAATTT
1 TAAAAGTTTTGGAAAAAAAAAATTT
31895606 T
1 T
31895607 CAAGGAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (25 bp):
TAAAAGTTTTGGAAAAAAAAAATTT
Found at i:31896042 original size:28 final size:28
Alignment explanation
Indices: 31895985--31896049 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 28
31895975 TACAATTAAC
* *
31895985 AACCAATTTGGATTCACATTAAAAAAAA
1 AACCAATTTAGATTCAAATTAAAAAAAA
* *
31896013 AACCAATTTAGATTCTAAATTTAAAGAAA
1 AACCAATTTAGATTC-AAATTAAAAAAAA
*
31896042 AACAAATT
1 AACCAATT
31896050 AGTTTAGGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.28
Consensus pattern (28 bp):
AACCAATTTAGATTCAAATTAAAAAAAA
Found at i:31899660 original size:7 final size:7
Alignment explanation
Indices: 31899648--31899689 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
31899638 AGAAAATAAT
31899648 TTTTTTC
1 TTTTTTC
31899655 TTTTTTTC
1 -TTTTTTC
31899663 TTTTTTC
1 TTTTTTC
*
31899670 TTTTTTT
1 TTTTTTC
31899677 TTTCTTTC
1 TTT-TTTC
31899685 TTTTT
1 TTTTT
31899690 CCAATTTTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
7 18 0.58
8 13 0.42
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:31899660 original size:8 final size:8
Alignment explanation
Indices: 31899647--31899689 Score: 63
Period size: 8 Copynumber: 5.6 Consensus size: 8
31899637 TAGAAAATAA
31899647 TTTTTTTC
1 TTTTTTTC
31899655 TTTTTTTC
1 TTTTTTTC
31899663 -TTTTTTC
1 TTTTTTTC
31899670 TTTTTTT-
1 TTTTTTTC
*
31899677 TTTCTTTC
1 TTTTTTTC
31899685 TTTTT
1 TTTTT
31899690 CCAATTTTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 13 0.42
8 18 0.58
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTC
Found at i:31899668 original size:15 final size:14
Alignment explanation
Indices: 31899647--31899689 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 14
31899637 TAGAAAATAA
31899647 TTTTTTTCTTTTTT
1 TTTTTTTCTTTTTT
31899661 TCTTTTTTCTTTTTT
1 T-TTTTTTCTTTTTT
31899676 TTTTCTTTCTTTTT
1 TTTT-TTTCTTTTT
31899690 CCAATTTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTCTTTTTT
Found at i:31899684 original size:22 final size:23
Alignment explanation
Indices: 31899647--31899689 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
31899637 TAGAAAATAA
*
31899647 TTTTTTTCTTTTTTTCTTTTTTC
1 TTTTTTTCTTTCTTTCTTTTTTC
31899670 TTTTTTT-TTTCTTTCTTTTT
1 TTTTTTTCTTTCTTTCTTTTT
31899690 CCAATTTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (23 bp):
TTTTTTTCTTTCTTTCTTTTTTC
Found at i:31899697 original size:22 final size:23
Alignment explanation
Indices: 31899649--31899702 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
31899639 GAAAATAATT
* * *
31899649 TTTTTCTTTTTTTCTTTTTTC-T
1 TTTTTCTTTCTTTCTTTTTCCAA
*
31899671 TTTTTTTTTCTTTCTTTTTCCAA
1 TTTTTCTTTCTTTCTTTTTCCAA
*
31899694 TTTTCCTTT
1 TTTTTCTTT
31899703 TTCAAGTGAC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTCTTTCTTTCTTTTTCCAA
Found at i:31900298 original size:17 final size:17
Alignment explanation
Indices: 31900259--31900316 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
31900249 ATATATATGG
**
31900259 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* *
31900276 AGATGCAGTGACAATAA
1 AAATGCAATGACAATAA
31900293 AAATGCAATGA-AATTAA
1 AAATGCAATGACAA-TAA
*
31900310 TAATGCA
1 AAATGCA
31900317 GGGACAATTA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
16 2 0.06
17 31 0.94
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.22
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:31904278 original size:14 final size:13
Alignment explanation
Indices: 31904259--31904305 Score: 60
Period size: 12 Copynumber: 3.5 Consensus size: 13
31904249 AGCAAACATT
31904259 TTTTTCTTCTTTTC
1 TTTTTC-TCTTTTC
31904273 TTTTTCT-TTTTC
1 TTTTTCTCTTTTC
31904285 TTTTTCTCATTTTCC
1 TTTTTCTC-TTTT-C
31904300 TTTTTC
1 TTTTTC
31904306 AAGTGACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 12 0.40
13 1 0.03
14 10 0.33
15 7 0.23
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTCTCTTTTC
Found at i:31904297 original size:20 final size:21
Alignment explanation
Indices: 31904259--31904305 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
31904249 AGCAAACATT
*
31904259 TTTTTCTTCTTTTC-TTTTTC
1 TTTTTCTTCTTTTCATTTTCC
31904279 TTTTTCTT-TTTCTCATTTTCC
1 TTTTTCTTCTTT-TCATTTTCC
31904300 TTTTTC
1 TTTTTC
31904306 AAGTGACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 3 0.12
20 10 0.42
21 11 0.46
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTTCTTCTTTTCATTTTCC
Found at i:31913975 original size:30 final size:30
Alignment explanation
Indices: 31913935--31914009 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
31913925 CTTAAGACGT
* *
31913935 CACCATCACCACCA-TAGGAAGAAAAGCATC
1 CACCACCACCACCACTAGG-AGAAAAACATC
*
31913965 CACCACCACCACCACTAGGAGAAAAACATT
1 CACCACCACCACCACTAGGAGAAAAACATC
*
31913995 CACCACCTCCACCAC
1 CACCACCACCACCAC
31914010 CGGAAAGAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 36 0.90
31 4 0.10
ACGTcount: A:0.40, C:0.41, G:0.09, T:0.09
Consensus pattern (30 bp):
CACCACCACCACCACTAGGAGAAAAACATC
Found at i:31914160 original size:24 final size:24
Alignment explanation
Indices: 31914133--31914184 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
31914123 CCTCAAAGCA
*
31914133 CTCCAACACAACAATCACCATCAT
1 CTCCAACACAACAATCACCACCAT
* *
31914157 CTCCTACCCAACAATCACCACCAT
1 CTCCAACACAACAATCACCACCAT
31914181 CTCC
1 CTCC
31914185 TAACCCTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.00, T:0.17
Consensus pattern (24 bp):
CTCCAACACAACAATCACCACCAT
Found at i:31914185 original size:24 final size:24
Alignment explanation
Indices: 31914141--31914186 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
31914131 CACTCCAACA
*
31914141 CAACAATCACCATCATCTCCTACC
1 CAACAATCACCACCATCTCCTACC
31914165 CAACAATCACCACCATCTCCTA
1 CAACAATCACCACCATCTCCTA
31914187 ACCCTCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.46, G:0.00, T:0.20
Consensus pattern (24 bp):
CAACAATCACCACCATCTCCTACC
Found at i:31916577 original size:21 final size:21
Alignment explanation
Indices: 31916560--31916600 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
31916550 CCCTAAACTC
31916560 TAAATCCAAAATCTTAAACCT
1 TAAATCCAAAATCTTAAACCT
*
31916581 TAAATCCAAAATCTAAAACC
1 TAAATCCAAAATCTTAAACC
31916601 CCAAACTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAATCCAAAATCTTAAACCT
Found at i:31925623 original size:2 final size:2
Alignment explanation
Indices: 31925616--31925642 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31925606 AATTTGTAAT
31925616 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 T
31925643 GAATTCAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31933622 original size:29 final size:29
Alignment explanation
Indices: 31933590--31933835 Score: 165
Period size: 30 Copynumber: 8.3 Consensus size: 29
31933580 AAAAATGAAG
31933590 TTTAGAAGAA-TTTGGGGTTAAAATGTGAT
1 TTTAGAA-AAGTTTGGGGTTAAAATGTGAT
* *
31933619 TTTAGAAAAGTTTGAGGGTGAAAACGTGAT
1 TTTAGAAAAGTTTG-GGGTTAAAATGTGAT
* * *
31933649 TTTGGAAAGGTTTGGGGGTCAAAATGTGAT
1 TTTAGAAAAGTTT-GGGGTTAAAATGTGAT
* * *
31933679 TTTGGAAAAGTTTGGGAGTTAAAATATAAT
1 TTTAGAAAAGTTTGGG-GTTAAAATGTGAT
* * ** * *
31933709 TTTAG-AATGTTTAGGGGTCAAAACATAAC
1 TTTAGAAAAGTTT-GGGGTTAAAATGTGAT
* * *
31933738 TTTGGAATAGTTTAGGGGTT-AAATGTAAT
1 TTTAGAAAAGTTT-GGGGTTAAAATGTGAT
* * * *
31933767 TTTGGGGAAAGTTTGAGAGTTAAAATGTAAT
1 TTT-AGAAAAGTTTG-GGGTTAAAATGTGAT
* * * *
31933798 TTTGGAAAAGTTTAAGGGTCAAAATGTAAT
1 TTTAGAAAAGTTT-GGGGTTAAAATGTGAT
31933828 TTTAGAAA
1 TTTAGAAA
31933836 TAAAAAAGGG
Statistics
Matches: 177, Mismatches: 30, Indels: 19
0.78 0.13 0.08
Matches are distributed among these distances:
28 2 0.01
29 44 0.25
30 118 0.67
31 13 0.07
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (29 bp):
TTTAGAAAAGTTTGGGGTTAAAATGTGAT
Found at i:31933711 original size:60 final size:58
Alignment explanation
Indices: 31933603--31933835 Score: 207
Period size: 60 Copynumber: 3.9 Consensus size: 58
31933593 AGAAGAATTT
* * * * * *
31933603 GGGGTTAAAATGTGATTTTAGAAAAGTTTGAGGGTGAAAACGTGATTTTGGAAAGGTTTG
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTG-GGGTTAAAATGTAATTTTGGAAA-GTTTG
* * * * *
31933663 GGGGTCAAAATGTGATTTTGGAAAAGTTTGGGAGTTAAAATATAATTTTAGAATGTTTA
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTGGG-GTTAAAATGTAATTTTGGAAAGTTTG
** * *
31933722 GGGGTCAAAACATAACTTTGGAATAGTTTAGGGGTT-AAATGTAATTTTGGGGAAAGTTTG
1 GGGGTCAAAATGTAATTTTGGAAAAGTTT-GGGGTTAAAATGTAATTTT--GGAAAGTTTG
* * * * * *
31933782 AGAGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTAGAAA
1 GGGGTCAAAATGTAATTTTGGAAAAGTTT-GGGGTTAAAATGTAATTTTGGAAA
31933836 TAAAAAAGGG
Statistics
Matches: 140, Mismatches: 28, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
58 11 0.08
59 37 0.26
60 80 0.57
61 12 0.09
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (58 bp):
GGGGTCAAAATGTAATTTTGGAAAAGTTTGGGGTTAAAATGTAATTTTGGAAAGTTTG
Found at i:31934783 original size:26 final size:25
Alignment explanation
Indices: 31934754--31934803 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
31934744 TTTAAATCTG
31934754 TTTTTAATATT-TTTATATTTATTTAC
1 TTTTTAAT-TTATTTATATTT-TTTAC
*
31934780 TTTTTTATTTATTTATATTTTTTA
1 TTTTTAATTTATTTATATTTTTTA
31934804 AACTCGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTTTAATTTATTTATATTTTTTAC
Found at i:31934788 original size:16 final size:17
Alignment explanation
Indices: 31934763--31934794 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
31934753 GTTTTTAATA
31934763 TTTTTATATTTATTTAC
1 TTTTTATATTTATTTAC
31934780 TTTTT-TATTTATTTA
1 TTTTTATATTTATTTA
31934795 TATTTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTATATTTATTTAC
Found at i:31937250 original size:26 final size:26
Alignment explanation
Indices: 31937216--31937267 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
31937206 GTCATTTGGA
31937216 TTTTCATTCTTGAGGATGAACGCTAT
1 TTTTCATTCTTGAGGATGAACGCTAT
* *
31937242 TTTTCATTCTTGGGGATGAATGCTAT
1 TTTTCATTCTTGAGGATGAACGCTAT
31937268 GAAAGATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.44
Consensus pattern (26 bp):
TTTTCATTCTTGAGGATGAACGCTAT
Found at i:31939188 original size:39 final size:40
Alignment explanation
Indices: 31939134--31939213 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 40
31939124 TATGCAATAA
*
31939134 ATGGACACCTTTTGAAGAGTCATAA-TCCTTTCAAATTGG
1 ATGGACACCTTTTGAAGAGTCACAACTCCTTTCAAATTGG
* * *
31939173 ATGGACACCTTTTGAAGGGTCACAACTCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACTCCTTTCAAATTGG
31939213 A
1 A
31939214 CATACCTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 23 0.64
40 13 0.36
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACTCCTTTCAAATTGG
Found at i:31944141 original size:39 final size:40
Alignment explanation
Indices: 31944087--31944166 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 40
31944077 TATGCACTCA
*
31944087 ATGGACACCTTTTGAAGAGTCATAA-TCCTTTCAAATTGG
1 ATGGACACCTTTTGAAGAGTCACAACTCCTTTCAAATTGG
* * *
31944126 ATGGACACCTTTTGAAGGGTCACAACTCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACTCCTTTCAAATTGG
31944166 A
1 A
31944167 CATACCTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 23 0.64
40 13 0.36
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACTCCTTTCAAATTGG
Found at i:31944861 original size:42 final size:42
Alignment explanation
Indices: 31944803--31944929 Score: 236
Period size: 42 Copynumber: 3.0 Consensus size: 42
31944793 GACCATATTA
* *
31944803 TACTACTATTTCCAAATTCTCCTTCAACTAAATTTCCATTGC
1 TACTACTCTTTCCAAATTCCCCTTCAACTAAATTTCCATTGC
31944845 TACTACTCTTTCCAAATTCCCCTTCAACTAAATTTCCATTGC
1 TACTACTCTTTCCAAATTCCCCTTCAACTAAATTTCCATTGC
31944887 TACTACTCTTTCCAAATTCCCCTTCAACTAAATTTCCATTGC
1 TACTACTCTTTCCAAATTCCCCTTCAACTAAATTTCCATTGC
31944929 T
1 T
31944930 TCCTAAACAT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 83 1.00
ACGTcount: A:0.27, C:0.31, G:0.02, T:0.39
Consensus pattern (42 bp):
TACTACTCTTTCCAAATTCCCCTTCAACTAAATTTCCATTGC
Found at i:31944874 original size:25 final size:25
Alignment explanation
Indices: 31944846--31944916 Score: 59
Period size: 25 Copynumber: 3.2 Consensus size: 25
31944836 TTCCATTGCT
31944846 ACTACTCTTTCCAAATTCCCCTTCA
1 ACTACTCTTTCCAAATTCCCCTTCA
** *
31944871 ACTA-AATTTCC--ATT--GC-T--
1 ACTACTCTTTCCAAATTCCCCTTCA
31944888 ACTACTCTTTCCAAATTCCCCTTCA
1 ACTACTCTTTCCAAATTCCCCTTCA
31944913 ACTA
1 ACTA
31944917 AATTTCCATT
Statistics
Matches: 32, Mismatches: 6, Indels: 16
0.59 0.11 0.30
Matches are distributed among these distances:
17 4 0.12
18 5 0.16
19 1 0.03
20 4 0.12
22 4 0.12
23 1 0.03
24 5 0.16
25 8 0.25
ACGTcount: A:0.27, C:0.35, G:0.01, T:0.37
Consensus pattern (25 bp):
ACTACTCTTTCCAAATTCCCCTTCA
Found at i:31947303 original size:29 final size:29
Alignment explanation
Indices: 31947269--31947363 Score: 102
Period size: 29 Copynumber: 3.3 Consensus size: 29
31947259 AGATATTGCT
31947269 ACAAAGGCATTCATTTAACAGAGATCGCC
1 ACAAAGGCATTCATTTAACAGAGATCGCC
* * * **
31947298 ATAAAGCCATTTCCTTT-ACAGAGATTACC
1 ACAAAGGCA-TTCATTTAACAGAGATCGCC
* * *
31947327 ACAAATGCATTCTTTTAACAAAGATCGCC
1 ACAAAGGCATTCATTTAACAGAGATCGCC
31947356 ACAAAGGC
1 ACAAAGGC
31947364 GTTTCCTTTT
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
28 6 0.12
29 39 0.76
30 6 0.12
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (29 bp):
ACAAAGGCATTCATTTAACAGAGATCGCC
Found at i:31947331 original size:58 final size:59
Alignment explanation
Indices: 31947252--31947394 Score: 175
Period size: 58 Copynumber: 2.5 Consensus size: 59
31947242 ATAAGGGATT
* * * *
31947252 CTTTTACAGATATTGCTACAAAGGCATTCATTTAACAGAGATCGCCATAAAGCCATTTC
1 CTTTTACAGAGATTGCCACAAAGGCATTCATTTAACAAAGATCGCCACAAAGCCATTTC
* * * * *
31947311 C-TTTACAGAGATTACCACAAATGCATTCTTTTAACAAAGATCGCCACAAAGGCGTTTC
1 CTTTTACAGAGATTGCCACAAAGGCATTCATTTAACAAAGATCGCCACAAAGCCATTTC
*
31947369 CTTTTA-A-AGCTTGCCACAAAGGCATT
1 CTTTTACAGAGATTGCCACAAAGGCATT
31947395 TCCTTTCAGA
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
57 16 0.23
58 50 0.70
59 5 0.07
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (59 bp):
CTTTTACAGAGATTGCCACAAAGGCATTCATTTAACAAAGATCGCCACAAAGCCATTTC
Found at i:31947384 original size:28 final size:27
Alignment explanation
Indices: 31947353--31947604 Score: 148
Period size: 28 Copynumber: 8.7 Consensus size: 27
31947343 AACAAAGATC
*
31947353 GCCACAAAGGCGTTTCCTTTTAAAGCTT
1 GCCACAAAGGC-TTTCCTTTTAAAGGTT
* *
31947381 GCCACAAAGGCATTTCCTTTCAGAGGTT
1 GCCACAAAGGC-TTTCCTTTTAAAGGTT
* *
31947409 CGCCACAAAGGCTTACCTTTCTAAAGTTT
1 -GCCACAAAGGCTTTCCTTT-TAAAGGTT
* * *
31947438 TCCA-AAGAGGTATTTCCTTTTAGAGGTT
1 GCCACAA-AGG-CTTTCCTTTTAAAGGTT
* * *
31947466 CGCCACAAGGGCTTACCTTTTCAAAGTTT
1 -GCCACAAAGGCTTTCCTTTT-AAAGGTT
* *
31947495 TCCACAAAGGCAGGCATTT-CTTTTCAGAGGTT
1 GCCAC-AA---AGGC-TTTCCTTTT-AAAGGTT
* *
31947527 CGCCACAAAGGCTTACCTTTTTAAAGTTT
1 -GCCACAAAGGCTTTCC-TTTTAAAGGTT
* *
31947556 GCCACAGAGGCATTTCCTTTCAAAGGTTT
1 GCCACAAAGGC-TTTCCTTTTAAAGG-TT
* * *
31947585 GTCGCAAAGGCTTACCTTTT
1 GCCACAAAGGCTTTCCTTTT
31947605 GATAATTTAT
Statistics
Matches: 170, Mismatches: 37, Indels: 34
0.71 0.15 0.14
Matches are distributed among these distances:
27 2 0.01
28 81 0.48
29 59 0.35
30 6 0.04
32 16 0.09
33 6 0.04
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (27 bp):
GCCACAAAGGCTTTCCTTTTAAAGGTT
Found at i:31947412 original size:57 final size:57
Alignment explanation
Indices: 31947351--31947604 Score: 316
Period size: 57 Copynumber: 4.4 Consensus size: 57
31947341 TTAACAAAGA
* *
31947351 TCGCCACAAAGGCGTTTCCTTTTAAAGCTTGCCACAA-AGGCATTTCCTTTCAGAGGT
1 TCGCCACAAAGGC-TTACCTTTTAAAGTTTGCCACAAGAGGCATTTCCTTTCAGAGGT
* * *
31947408 TCGCCACAAAGGCTTACCTTTCTAAAGTTTTCCA-AAGAGGTATTTCCTTTTAGAGGT
1 TCGCCACAAAGGCTTACCTTT-TAAAGTTTGCCACAAGAGGCATTTCCTTTCAGAGGT
* * *
31947465 TCGCCACAAGGGCTTACCTTTTCAAAGTTTTCCACAAAGGCAGGCATTTCTTTTCAGAGGT
1 TCGCCACAAAGGCTTACCTTTT-AAAGTTTGCCAC-AA-G-AGGCATTTCCTTTCAGAGGT
*
31947526 TCGCCACAAAGGCTTACCTTTTTAAAGTTTGCCAC-AGAGGCATTTCCTTTCAAAGGT
1 TCGCCACAAAGGCTTACC-TTTTAAAGTTTGCCACAAGAGGCATTTCCTTTCAGAGGT
* * *
31947583 TTGTCGCAAAGGCTTACCTTTT
1 TCGCCACAAAGGCTTACCTTTT
31947605 GATAATTTAT
Statistics
Matches: 173, Mismatches: 16, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
56 14 0.08
57 105 0.61
58 1 0.01
59 3 0.02
60 1 0.01
61 45 0.26
62 4 0.02
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (57 bp):
TCGCCACAAAGGCTTACCTTTTAAAGTTTGCCACAAGAGGCATTTCCTTTCAGAGGT
Found at i:31947531 original size:118 final size:118
Alignment explanation
Indices: 31947351--31947604 Score: 338
Period size: 118 Copynumber: 2.2 Consensus size: 118
31947341 TTAACAAAGA
* * *
31947351 TCGCCACAAAGGCGTTTCCTTTT-AAAGCTTGCCAC-AA---AGGCATTTCCTTTCAGAGGTTCG
1 TCGCCACAAAGGC-TTACCTTTTCAAAGTTTTCCACAAAGGCAGGCATTTCCTTTCAGAGGTTCG
* * * *
31947411 CCACAAAGGCTTACCTTTCTAAAGTTTTCCAAAGAGGTATTTCCTTTTAGAGGT
65 CCACAAAGGCTTACCTTTCTAAAGTTTGCCAAAGAGGCATTTCCTTTCAAAGGT
* *
31947465 TCGCCACAAGGGCTTACCTTTTCAAAGTTTTCCACAAAGGCAGGCATTTCTTTTCAGAGGTTCGC
1 TCGCCACAAAGGCTTACCTTTTCAAAGTTTTCCACAAAGGCAGGCATTTCCTTTCAGAGGTTCGC
* *
31947530 CACAAAGGCTTACCTTTTTAAAGTTTGCCACAGAGGCATTTCCTTTCAAAGGT
66 CACAAAGGCTTACCTTTCTAAAGTTTGCCAAAGAGGCATTTCCTTTCAAAGGT
* * *
31947583 TTGTCGCAAAGGCTTACCTTTT
1 TCGCCACAAAGGCTTACCTTTT
31947605 GATAATTTAT
Statistics
Matches: 120, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
113 8 0.07
114 22 0.18
115 2 0.02
118 88 0.73
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (118 bp):
TCGCCACAAAGGCTTACCTTTTCAAAGTTTTCCACAAAGGCAGGCATTTCCTTTCAGAGGTTCGC
CACAAAGGCTTACCTTTCTAAAGTTTGCCAAAGAGGCATTTCCTTTCAAAGGT
Found at i:31947905 original size:15 final size:15
Alignment explanation
Indices: 31947868--31947924 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
31947858 GGAGATAGAC
31947868 ACAAACTCA-TCAT-
1 ACAAACTCATTCATA
31947881 ACATAGACTCATTCATA
1 ACA-A-ACTCATTCATA
* * *
31947898 ACACACTCGTTCATG
1 ACAAACTCATTCATA
31947913 ACAAACTCATTC
1 ACAAACTCATTC
31947925 CTTTTTTTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 3 0.09
14 1 0.03
15 24 0.69
16 4 0.11
17 3 0.09
ACGTcount: A:0.39, C:0.30, G:0.05, T:0.26
Consensus pattern (15 bp):
ACAAACTCATTCATA
Found at i:31950214 original size:52 final size:52
Alignment explanation
Indices: 31950136--31950284 Score: 199
Period size: 52 Copynumber: 2.9 Consensus size: 52
31950126 TAAATGAAAA
* *
31950136 AGGTCCGATGACTATGTATCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
31950188 AGGTCCGATGACTATATGTTATCGTGAGTATATGAATTCTTCACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * * *
31950240 AGGTTCGGTGACTATGTGTCATCGTGGGTGTATGATTCCTTTACG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACG
31950285 AAATAAGGAT
Statistics
Matches: 82, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 82 1.00
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:31957467 original size:52 final size:52
Alignment explanation
Indices: 31957367--31957551 Score: 212
Period size: 52 Copynumber: 3.6 Consensus size: 52
31957357 AAATGAAAAG
* *
31957367 GGTCCGATGACTATGTGTCAT-GTGAGTATATGAATCCTTTACAGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAACCCTTCACAGATTATGA
* *
31957418 GGTCCAATGACTATGTTTCATCGTGAGTATATGAACCCTTCA-AGAATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAACCCTTCACAG-ATTATGA
* * * ** * * ** *
31957470 GGTCTGATGACTATGCGTCATCGTGAGTGTATGATTCCTTTACGGAACAAGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAACCCTTCACAGATTATGA
*
31957522 GGTCCGATGACTATGTGCCATCGTGAGTAT
1 GGTCCGATGACTATGTGTCATCGTGAGTAT
31957552 TAAATGAAAT
Statistics
Matches: 111, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
51 21 0.19
52 89 0.80
53 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (52 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATGAACCCTTCACAGATTATGA
Found at i:31958656 original size:7 final size:7
Alignment explanation
Indices: 31958644--31958671 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
31958634 TTGTATAAAG
31958644 AAATATA
1 AAATATA
31958651 AAATATA
1 AAATATA
31958658 AAATATA
1 AAATATA
31958665 AAATATA
1 AAATATA
31958672 GAAAATCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAATATA
Found at i:31960753 original size:18 final size:18
Alignment explanation
Indices: 31960732--31960768 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
31960722 AAAATTAATT
31960732 TTAAATATGGTTCTAAAA
1 TTAAATATGGTTCTAAAA
*
31960750 TTAAATATGGTTGTAAAA
1 TTAAATATGGTTCTAAAA
31960768 T
1 T
31960769 ATTTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.41
Consensus pattern (18 bp):
TTAAATATGGTTCTAAAA
Found at i:31960796 original size:32 final size:33
Alignment explanation
Indices: 31960745--31960850 Score: 124
Period size: 33 Copynumber: 3.2 Consensus size: 33
31960735 AATATGGTTC
31960745 TAAAATTAAATATGGTTGTAAAATATTTAATTT
1 TAAAATTAAATATGGTTGTAAAATATTTAATTT
* * * *
31960778 TAAAATT-ATTTTGGTTGTAAAATAAATTAAATT
1 TAAAATTAAATATGGTTGTAAAAT-ATTTAATTT
* ** *
31960811 AAAAATTAAATATAATTGTAAAATATTTGATTT
1 TAAAATTAAATATGGTTGTAAAATATTTAATTT
31960844 TAAAATT
1 TAAAATT
31960851 TAATTTAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
32 14 0.24
33 32 0.55
34 12 0.21
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (33 bp):
TAAAATTAAATATGGTTGTAAAATATTTAATTT
Found at i:31960867 original size:66 final size:66
Alignment explanation
Indices: 31960746--31960874 Score: 163
Period size: 66 Copynumber: 2.0 Consensus size: 66
31960736 ATATGGTTCT
** ****
31960746 AAAATTAAATATGGTTGTAAAATATTTAATTTTAAAATTATTTTGGTTGTAAAATAAATTAAATT
1 AAAATTAAATATAATTGTAAAATATTTAATTTTAAAATTATTTAAAATGTAAAATAAATTAAATT
31960811 A
66 A
*
31960812 AAAATTAAATATAATTGTAAAATATTTGATTTTAAAATTTAATTTAAAAT-T-AAATAAATTAAA
1 AAAATTAAATATAATTGTAAAATATTTAATTTTAAAA-TT-ATTTAAAATGTAAAATAAATTAAA
31960875 ATCAACTTGA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
66 46 0.85
67 3 0.06
68 5 0.09
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (66 bp):
AAAATTAAATATAATTGTAAAATATTTAATTTTAAAATTATTTAAAATGTAAAATAAATTAAATT
A
Found at i:31960894 original size:45 final size:45
Alignment explanation
Indices: 31960801--31960892 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 45
31960791 GTTGTAAAAT
*
31960801 AAATTAAATTAAAAATTAAATATAATTGTAAAATATTTGATTTTA
1 AAATTAAATTAAAAATTAAATATAATTGTAAAATACTTGATTTTA
* *
31960846 AAATTTAATTTAAAATTAAATA-AA-T-TAAAATCAACTTGATTTTA
1 AAATTAAATTAAAAATTAAATATAATTGTAAAAT--ACTTGATTTTA
31960890 AAA
1 AAA
31960893 ATCGAAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
42 6 0.14
43 1 0.02
44 15 0.36
45 20 0.48
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.40
Consensus pattern (45 bp):
AAATTAAATTAAAAATTAAATATAATTGTAAAATACTTGATTTTA
Found at i:31961425 original size:51 final size:51
Alignment explanation
Indices: 31961339--31961436 Score: 117
Period size: 51 Copynumber: 1.9 Consensus size: 51
31961329 TACTCTAATA
** * * *
31961339 TAAATATTAAAATAATGTTAAGATAACTATATAAAAAATATATAAAATTAT
1 TAAATATTAAAATAATAATAAAATAAATATATAAAAAAAATATAAAATTAT
* *
31961390 TAAATATTAAAATAA-AATAAAATAAATATTTTAAAAAAAATTTAAAA
1 TAAATATTAAAATAATAATAAAATAAATA-TATAAAAAAAATATAAAA
31961437 ATAATTTAGG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 9 0.23
51 30 0.77
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (51 bp):
TAAATATTAAAATAATAATAAAATAAATATATAAAAAAAATATAAAATTAT
Found at i:31967249 original size:15 final size:17
Alignment explanation
Indices: 31967220--31967252 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
31967210 AAAATTTTAA
31967220 TAAATATATATAATTAT
1 TAAATATATATAATTAT
31967237 TAAATAT-TA-AATTAT
1 TAAATATATATAATTAT
31967252 T
1 T
31967253 TTTAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAATATATATAATTAT
Found at i:31969989 original size:17 final size:17
Alignment explanation
Indices: 31969969--31970004 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
31969959 TTTATTATGA
31969969 AATTGTGGTGGGAATAG
1 AATTGTGGTGGGAATAG
31969986 AATTGTGGTGGGAATAG
1 AATTGTGGTGGGAATAG
31970003 AA
1 AA
31970005 AGTATAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.39, T:0.28
Consensus pattern (17 bp):
AATTGTGGTGGGAATAG
Found at i:31970721 original size:38 final size:38
Alignment explanation
Indices: 31970650--31970729 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
31970640 ATGCACTAGG
* **
31970650 ATGCGCTTTATGCACCAGGATGCATTTTGTGCGCCAAT
1 ATGCGCTTTATGCACCAAGATGCATTTCATGCGCCAAT
* ** *
31970688 ATGCGCTTTGTGCACCAAGATGTGTTTCATGCGCTAAT
1 ATGCGCTTTATGCACCAAGATGCATTTCATGCGCCAAT
31970726 ATGC
1 ATGC
31970730 ATCTTACGTG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.33
Consensus pattern (38 bp):
ATGCGCTTTATGCACCAAGATGCATTTCATGCGCCAAT
Found at i:31986167 original size:21 final size:23
Alignment explanation
Indices: 31986141--31986182 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
31986131 TATAGTCTAT
*
31986141 TATAAAA-TA-TATATTATATGC
1 TATAAAAGTATTATAATATATGC
31986162 TATAAAAGTATTATAATATAT
1 TATAAAAGTATTATAATATAT
31986183 TTATTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 2 0.11
23 9 0.50
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (23 bp):
TATAAAAGTATTATAATATATGC
Found at i:31986912 original size:12 final size:12
Alignment explanation
Indices: 31986895--31986987 Score: 64
Period size: 12 Copynumber: 7.8 Consensus size: 12
31986885 ATAACATTCA
31986895 AACAACAAAAAT
1 AACAACAAAAAT
* *
31986907 AACAACCAAAAC
1 AACAACAAAAAT
* **
31986919 AGCAGTAAAAAT
1 AACAACAAAAAT
* **
31986931 GAC-AGTAAAAT
1 AACAACAAAAAT
*
31986942 AGCAACAAAAAT
1 AACAACAAAAAT
31986954 AACAACAAAAAT
1 AACAACAAAAAT
* *
31986966 AAC-ACGAAAAC
1 AACAACAAAAAT
31986977 AACAATCAAAA
1 AACAA-CAAAA
31986988 TAGTAAAAAA
Statistics
Matches: 58, Mismatches: 20, Indels: 5
0.70 0.24 0.06
Matches are distributed among these distances:
11 15 0.26
12 39 0.67
13 4 0.07
ACGTcount: A:0.67, C:0.18, G:0.06, T:0.09
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:31986963 original size:23 final size:24
Alignment explanation
Indices: 31986897--31986990 Score: 75
Period size: 23 Copynumber: 4.0 Consensus size: 24
31986887 AACATTCAAA
*
31986897 CAACAAAAATAACAACCAAAACAG
1 CAACAAAAATAACAACCAAAATAG
** * **
31986921 CAGTAAAAATGAC-AGTAAAATAG
1 CAACAAAAATAACAACCAAAATAG
* *
31986944 CAACAAAAATAACAACAAAAATAA
1 CAACAAAAATAACAACCAAAATAG
* * *
31986968 C-ACGAAAACAACAATCAAAATAG
1 CAACAAAAATAACAACCAAAATAG
31986991 TAAAAAACAA
Statistics
Matches: 52, Mismatches: 17, Indels: 3
0.72 0.24 0.04
Matches are distributed among these distances:
23 34 0.65
24 18 0.35
ACGTcount: A:0.65, C:0.18, G:0.07, T:0.10
Consensus pattern (24 bp):
CAACAAAAATAACAACCAAAATAG
Found at i:31987015 original size:20 final size:19
Alignment explanation
Indices: 31986972--31987016 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
31986962 AAATAACACG
* *
31986972 AAAACAACAATCAAAATAGT
1 AAAA-AACAATCAAAAAAGC
31986992 AAAAAACAATACAAAAAAGC
1 AAAAAACAAT-CAAAAAAGC
31987012 AAAAA
1 AAAAA
31987017 CAGCAACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.73, C:0.13, G:0.04, T:0.09
Consensus pattern (19 bp):
AAAAAACAATCAAAAAAGC
Found at i:31989679 original size:21 final size:22
Alignment explanation
Indices: 31989654--31989696 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
31989644 AAAATTTTGA
31989654 ATTTTATGAATTTTT-TATTTT
1 ATTTTATGAATTTTTGTATTTT
*
31989675 ATTTTTTGAATTTTTGTATTTT
1 ATTTTATGAATTTTTGTATTTT
31989697 TAATAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (22 bp):
ATTTTATGAATTTTTGTATTTT
Found at i:31989689 original size:22 final size:21
Alignment explanation
Indices: 31989654--31989696 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
31989644 AAAATTTTGA
*
31989654 ATTTTATGAATTTTTTATTTT
1 ATTTTATGAATTTTGTATTTT
*
31989675 ATTTTTTGAATTTTTGTATTTT
1 ATTTTATGAA-TTTTGTATTTT
31989697 TAATAATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (21 bp):
ATTTTATGAATTTTGTATTTT
Found at i:31990660 original size:19 final size:20
Alignment explanation
Indices: 31990624--31990665 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
31990614 ATTCAAAGAT
31990624 AAAAAGTCTAAAAGAAAACA
1 AAAAAGTCTAAAAGAAAACA
* *
31990644 AAAAAGTTTCAAA-AAAACA
1 AAAAAGTCTAAAAGAAAACA
31990663 AAA
1 AAA
31990666 TATAAAAGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.71, C:0.10, G:0.07, T:0.12
Consensus pattern (20 bp):
AAAAAGTCTAAAAGAAAACA
Found at i:32007295 original size:43 final size:43
Alignment explanation
Indices: 32007171--32007344 Score: 174
Period size: 43 Copynumber: 4.1 Consensus size: 43
32007161 GAAAAACGTT
* * * *
32007171 GCTATAGAACAT-GATCTTTAGTGGTGCTTTT-GCACAAACGCC
1 GCTAAAGAACATCG-TCTTTAGCGGCGCTTTTCTCACAAACGCC
* * ** *
32007213 GCTAAAGAACATGGTC-TTAGTGGCGCTTTTAGCACAAACGTC
1 GCTAAAGAACATCGTCTTTAGCGGCGCTTTTCTCACAAACGCC
* *
32007255 GCTAAAGAACAACGTCTTTAGCGGCGCTTTTCTAACAAACGCC
1 GCTAAAGAACATCGTCTTTAGCGGCGCTTTTCTCACAAACGCC
* ** * *
32007298 GTTAAAGAACATTATCTTTAGCAGCGCTTTTCTCACAAACACC
1 GCTAAAGAACATCGTCTTTAGCGGCGCTTTTCTCACAAACGCC
32007341 GCTA
1 GCTA
32007345 CAAAAAATGG
Statistics
Matches: 111, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
41 13 0.12
42 37 0.33
43 61 0.55
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (43 bp):
GCTAAAGAACATCGTCTTTAGCGGCGCTTTTCTCACAAACGCC
Found at i:32007393 original size:14 final size:14
Alignment explanation
Indices: 32007374--32007403 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
32007364 ATTTTACCAC
32007374 AAACGCCACTAAAG
1 AAACGCCACTAAAG
*
32007388 AAACGCCGCTAAAG
1 AAACGCCACTAAAG
32007402 AA
1 AA
32007404 CATGGGCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.27, G:0.17, T:0.07
Consensus pattern (14 bp):
AAACGCCACTAAAG
Found at i:32007460 original size:97 final size:99
Alignment explanation
Indices: 32007291--32007479 Score: 231
Period size: 97 Copynumber: 1.9 Consensus size: 99
32007281 CTTTTCTAAC
* * *
32007291 AAACGCCGTTAAAGAACATTATCTTTAGCAGCGCTTTTCTCACAAACACCGCTACAAAAAATGGT
1 AAACGCCGCTAAAGAACATGAGCTTTAGCAGCGCTTTTCTCACAAACACCGCTACAAAAAATGGT
32007356 CTGTAGC-G-ATTTTACCACAAACGCCACTAAAG
66 CTGTAGCGGCATTTTACCACAAACGCCACTAAAG
* * * * ** * *
32007388 AAACGCCGCTAAAGAACATGGGCTTTAGCGGTGTTTTTCTCACAAACGTCGTTA-AAGAACATGG
1 AAACGCCGCTAAAGAACATGAGCTTTAGCAGCGCTTTTCTCACAAACACCGCTACAA-AAAATGG
* *
32007452 TCTTTAGCGGCATTTTCCCACAAACGCC
65 TCTGTAGCGGCATTTTACCACAAACGCC
32007480 GTTAAAATTA
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
96 2 0.03
97 57 0.75
98 1 0.01
99 16 0.21
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (99 bp):
AAACGCCGCTAAAGAACATGAGCTTTAGCAGCGCTTTTCTCACAAACACCGCTACAAAAAATGGT
CTGTAGCGGCATTTTACCACAAACGCCACTAAAG
Found at i:32007483 original size:42 final size:43
Alignment explanation
Indices: 32007388--32007485 Score: 135
Period size: 43 Copynumber: 2.3 Consensus size: 43
32007378 GCCACTAAAG
* ** *
32007388 AAACGCCGCTAAAGAACATGGGCTTTAGCGGTGTTTTTCTCAC
1 AAACGCCGTTAAAGAACATGGGCTTTAGCGGTCATTTTCCCAC
* *
32007431 AAACGTCGTTAAAGAACATGGTCTTTAGCGG-CATTTTCCCAC
1 AAACGCCGTTAAAGAACATGGGCTTTAGCGGTCATTTTCCCAC
32007473 AAACGCCGTTAAA
1 AAACGCCGTTAAA
32007486 ATTAATAGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 20 0.42
43 28 0.58
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (43 bp):
AAACGCCGTTAAAGAACATGGGCTTTAGCGGTCATTTTCCCAC
Found at i:32007894 original size:66 final size:66
Alignment explanation
Indices: 32007758--32007895 Score: 163
Period size: 66 Copynumber: 2.1 Consensus size: 66
32007748 TCATATTTTG
* ***
32007758 AAGTTGTAGCTACAGTTCGTCATACTTTCTTTGAGACTCTGCTTTCCTCGCTGCTGCCTTGGCTT
1 AAGTTGTAGCTACAGTTCGTCATACTTTCTTTGAGACTCTGCTTTCCTCGCTGCTACCTCCACTT
32007823 C
66 C
* * * *
32007824 AAGTTGTAGCTGA-AGTTTGTTATATTTTCTTTGAGCCTCTGC-TTCTCTCGCTGCTACCTCCAC
1 AAGTTGTAGCT-ACAGTTCGTCATACTTTCTTTGAGACTCTGCTTTC-CTCGCTGCTACCTCCAC
*
32007887 TTT
64 TTC
32007890 AAGTTG
1 AAGTTG
32007896 AGCAATTTAC
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
65 3 0.05
66 57 0.93
67 1 0.02
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.41
Consensus pattern (66 bp):
AAGTTGTAGCTACAGTTCGTCATACTTTCTTTGAGACTCTGCTTTCCTCGCTGCTACCTCCACTT
C
Found at i:32013672 original size:70 final size:70
Alignment explanation
Indices: 32013590--32013835 Score: 213
Period size: 70 Copynumber: 3.7 Consensus size: 70
32013580 ATAATTAAAT
32013590 AATTAAATATTTGGGTTGTTTTTAATAATTAAATATTTATTTAAATATAATTAAATAATTAAATA
1 AATTAAATATTTGGGTTGTTTTTAATAATTAAATATTTATTTAAATATAATTAAATAATTAAATA
32013655 TTTTG
66 TTTTG
** * * *** **
32013660 AATTAAATATTTGGGTTTAGGGTTTAATAAATAAATA---A-ATAAATAT--TTGGGTTGTTTTT
1 AATTAAATATTTGGG-TT-GTTTTTAATAATTAAATATTTATTTAAATATAATT---AAATAATT
32013719 AAATATTTTG
61 AAATATTTTG
*
32013729 AATTAAATA-TT---TTG--------AATTAAATATTTATTCAAATATAATTAAATAATTAAATA
1 AATTAAATATTTGGGTTGTTTTTAATAATTAAATATTTATTTAAATATAATTAAATAATTAAATA
32013782 TTTTG
66 TTTTG
* *
32013787 AATTATATATTTGGATTGTTTTTAATAATTAAATATTTATTTAAATATA
1 AATTAAATATTTGGGTTGTTTTTAATAATTAAATATTTATTTAAATATA
32013836 GAGGAATTAT
Statistics
Matches: 134, Mismatches: 19, Indels: 46
0.67 0.10 0.23
Matches are distributed among these distances:
55 8 0.06
58 22 0.16
59 8 0.06
61 2 0.01
62 3 0.02
63 1 0.01
64 2 0.01
66 2 0.01
68 9 0.07
69 23 0.17
70 37 0.28
71 2 0.01
72 15 0.11
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (70 bp):
AATTAAATATTTGGGTTGTTTTTAATAATTAAATATTTATTTAAATATAATTAAATAATTAAATA
TTTTG
Found at i:32013736 original size:14 final size:14
Alignment explanation
Indices: 32013717--32013754 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
32013707 TGGGTTGTTT
32013717 TTAAATATTTTGAA
1 TTAAATATTTTGAA
32013731 TTAAATATTTTGAA
1 TTAAATATTTTGAA
32013745 TTAAATATTT
1 TTAAATATTT
32013755 ATTCAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (14 bp):
TTAAATATTTTGAA
Found at i:32013790 original size:22 final size:22
Alignment explanation
Indices: 32013729--32013791 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
32013719 AAATATTTTG
32013729 AATTAAATATTTTGAATTAAAT
1 AATTAAATATTTTGAATTAAAT
32013751 ATTTATTCAAATA---T-AATTAAAT
1 A---ATT-AAATATTTTGAATTAAAT
32013773 AATTAAATATTTTGAATTA
1 AATTAAATATTTTGAATTA
32013792 TATATTTGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 16
0.67 0.00 0.33
Matches are distributed among these distances:
18 5 0.15
19 3 0.09
21 1 0.03
22 15 0.45
23 1 0.03
25 3 0.09
26 5 0.15
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (22 bp):
AATTAAATATTTTGAATTAAAT
Found at i:32014589 original size:13 final size:13
Alignment explanation
Indices: 32014571--32014595 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32014561 ATTCAATGTC
32014571 AACTACCATTTTG
1 AACTACCATTTTG
32014584 AACTACCATTTT
1 AACTACCATTTT
32014596 CATCAAAACA
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:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (13 bp):
AACTACCATTTTG
Found at i:32016165 original size:34 final size:34
Alignment explanation
Indices: 32016127--32016193 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
32016117 ACGTGAAGAA
* * * *
32016127 GTGAAGAAGATTCTAGCGTCCAGAAGAGAAGGGC
1 GTGAAGAAGAATCGAACGTCAAGAAGAGAAGGGC
* *
32016161 GTGAAGGAGAATCGAACGTGAAGAAGAGAAGGG
1 GTGAAGAAGAATCGAACGTCAAGAAGAGAAGGG
32016194 TGAGAGTAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.39, C:0.10, G:0.39, T:0.12
Consensus pattern (34 bp):
GTGAAGAAGAATCGAACGTCAAGAAGAGAAGGGC
Found at i:32016399 original size:42 final size:41
Alignment explanation
Indices: 32016347--32016435 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 41
32016337 TAGTGGCGTT
* *
32016347 TTTTTCATAAACGTCGCTAATGATCTGGATTTTTTGCGATA
1 TTTTTCATAAACGCCGCTAATGATCTGGATCTTTTGCGATA
* * * *
32016388 TTTTTCAATAAACGCCGCTATTGCTCTGGATCTTTTGCGGTG
1 TTTTTC-ATAAACGCCGCTAATGATCTGGATCTTTTGCGATA
32016430 TTTTTC
1 TTTTTC
32016436 TCATAAATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 6 0.15
42 35 0.85
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.45
Consensus pattern (41 bp):
TTTTTCATAAACGCCGCTAATGATCTGGATCTTTTGCGATA
Found at i:32017101 original size:22 final size:22
Alignment explanation
Indices: 32017076--32017117 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
32017066 AACATTTCTA
32017076 AAACCACAAAATTGATTAATAG
1 AAACCACAAAATTGATTAATAG
32017098 AAACCACAAAATTGATTAAT
1 AAACCACAAAATTGATTAAT
32017118 TCATATGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.24
Consensus pattern (22 bp):
AAACCACAAAATTGATTAATAG
Found at i:32018013 original size:41 final size:39
Alignment explanation
Indices: 32017940--32018163 Score: 170
Period size: 41 Copynumber: 5.6 Consensus size: 39
32017930 GTTTATGGGA
* * * *
32017940 AAACGCCGCTATTGCTTAACCTTTAACGGCGTTTTCCCAT
1 AAACGCCGCTAATGCTTTACCTTTAGC-GCGTTTTCTCAT
* *
32017980 AAATGCCGCTAATGCTCTTACCTTTAGCTGCGTTTTCTAAT
1 AAACGCCGCTAATGCT-TTACCTTTAGC-GCGTTTTCTCAT
** * * *
32018021 AAACGCTACTAATTCTCTGACCTTTAGCGGGATTTTCTCAT
1 AAACGCCGCTAATGCT-TTACCTTTAGCGCG-TTTTCTCAT
*
32018062 AAACGCCGCTAATTCTTTAACC--T-G-GCGTTTTCTCAT
1 AAACGCCGCTAATGCTTT-ACCTTTAGCGCGTTTTCTCAT
* * *
32018098 AAATGCCGCTAATGCTCTGACATTTAGCGGCGTTTT-TCCTAT
1 AAACGCCGCTAATGCT-TTACCTTTAGC-GCGTTTTCT-C-AT
* *
32018140 AAACGACGCTATTGCTTTACCTTT
1 AAACGCCGCTAATGCTTTACCTTT
32018164 TGCGACATTT
Statistics
Matches: 146, Mismatches: 27, Indels: 21
0.75 0.14 0.11
Matches are distributed among these distances:
36 25 0.17
37 3 0.02
38 2 0.01
39 2 0.01
40 18 0.12
41 81 0.55
42 15 0.10
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (39 bp):
AAACGCCGCTAATGCTTTACCTTTAGCGCGTTTTCTCAT
Found at i:32018124 original size:77 final size:78
Alignment explanation
Indices: 32018009--32018158 Score: 189
Period size: 77 Copynumber: 1.9 Consensus size: 78
32017999 ACCTTTAGCT
* * * *
32018009 GCGTTTTCTAATAAACGCTACTAATTCTCTGACCTTTAGCGG-GATTTT-CTCATAAACGCCGCT
1 GCGTTTTCTAATAAACGCCACTAATGCTCTGACATTTAGCGGCGATTTTCCT-ATAAACGACGCT
32018072 AATT-CTTTAACCTG
65 -ATTGCTTTAACCTG
* * * *
32018086 GCGTTTTCTCATAAATGCCGCTAATGCTCTGACATTTAGCGGCGTTTTTCCTATAAACGACGCTA
1 GCGTTTTCTAATAAACGCCACTAATGCTCTGACATTTAGCGGCGATTTTCCTATAAACGACGCTA
32018151 TTGCTTTA
66 TTGCTTTA
32018159 CCTTTTGCGA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
77 39 0.63
78 21 0.34
79 2 0.03
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (78 bp):
GCGTTTTCTAATAAACGCCACTAATGCTCTGACATTTAGCGGCGATTTTCCTATAAACGACGCTA
TTGCTTTAACCTG
Found at i:32030999 original size:30 final size:30
Alignment explanation
Indices: 32030908--32030999 Score: 157
Period size: 30 Copynumber: 3.1 Consensus size: 30
32030898 ATGCTCCCTA
*
32030908 TGGAGGTCATTTTGGTGGAATGAGGACTAC
1 TGGAGGTCATTTTGGTGGAATGAGGACTGC
32030938 TGGAGGTCATTTTGGTGGAATGAGGACTGC
1 TGGAGGTCATTTTGGTGGAATGAGGACTGC
* *
32030968 TGGAAGTCATTTTGGTGGAATGAGGATTGC
1 TGGAGGTCATTTTGGTGGAATGAGGACTGC
32030998 TG
1 TG
32031000 TAAAGGTCTT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.22, C:0.09, G:0.38, T:0.32
Consensus pattern (30 bp):
TGGAGGTCATTTTGGTGGAATGAGGACTGC
Found at i:32032086 original size:14 final size:14
Alignment explanation
Indices: 32032063--32032100 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
32032053 CATTTTTGCA
32032063 TTTCCTTTTATCT-
1 TTTCCTTTTATCTG
*
32032076 TTTCACTTTTATTTG
1 TTTC-CTTTTATCTG
32032091 TTTCCTTTTA
1 TTTCCTTTTA
32032101 AATTCTATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 14 0.64
15 4 0.18
ACGTcount: A:0.11, C:0.18, G:0.03, T:0.68
Consensus pattern (14 bp):
TTTCCTTTTATCTG
Found at i:32032883 original size:21 final size:21
Alignment explanation
Indices: 32032859--32032911 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
32032849 TTGTGCTAGC
32032859 TCTACCGATACAAGT-ATG-A
1 TCTACCGATACAAGTCATGCA
*
32032878 TTTCTACCAATACAAGTCATGCA
1 --TCTACCGATACAAGTCATGCA
32032901 TCTACCGATAC
1 TCTACCGATAC
32032912 TAAAAACTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 24 0.86
22 3 0.11
23 1 0.04
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.28
Consensus pattern (21 bp):
TCTACCGATACAAGTCATGCA
Found at i:32040030 original size:21 final size:22
Alignment explanation
Indices: 32039993--32040035 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
32039983 ATTTTAATCA
*
32039993 TTAAGCTTTAATTAACC-ATTT
1 TTAACCTTTAATTAACCTATTT
32040014 TTAACCTTT-ATTAAACCTATTT
1 TTAACCTTTAATT-AACCTATTT
32040036 ATAATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.16
21 12 0.63
22 4 0.21
ACGTcount: A:0.33, C:0.16, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAACCTTTAATTAACCTATTT
Found at i:32041914 original size:335 final size:335
Alignment explanation
Indices: 32041304--32041963 Score: 1104
Period size: 335 Copynumber: 2.0 Consensus size: 335
32041294 TGGAACGATA
* * *
32041304 CTATTGTCGCTACATTAAGGAGTATGAGCCCAAGTCCACTGCCAGATTTCCTTGTCTTCCCATCT
1 CTATTGTCACTACATTAAGGAGTATGAGCCCAAGTCCACTGCCAAATTTCCCTGTCTTCCCATCT
* * * * * *
32041369 ATCTTTCGACTAATGCCCTCATCCTCCGACCAGCCTACTCTTGATGGTAGGCCTCAACATGTCCC
66 ATCTTCCAACCAATGCCCTCATCCTCCGACCAACCTACTCTTAATGGTAGGCCTCAACACGTCCC
* *
32041434 CTCTCCAACGAGAATCCACATTTCAAATGACGAGAAGCACGAGGGGCATTCTAATGCTATGGAGG
131 CTCTCCAACGAGAATCCACATTTCAAATGACGAGAAGCACGAGAGGCAATCTAATGCTATGGAGG
*
32041499 ATTGCTACAGAACTATAGCCAGCTTATTCGAAGAAGAGTTCTCGAACAGCCTTAGGGCTAATATG
196 ATTGCTACAGAACTATAGCCAGCTTATTCGAAGAAGAGTTCTCAAACAGCCTTAGGGCTAATATG
* * * *
32041564 GTAGAGCGGGCAGCTATAGTTGAAGAGATGCATACCTCAGTTGTATCTATGGGTGTGGATGCAAA
261 GTAGAACGGGCAGCTATAGTTGAAAAGATGCATACCCCAGTTGTATCTATGGGTGTGGATACAAA
32041629 GGAAAGCACG
326 GGAAAGCACG
*
32041639 CTATTGTTACTACATTAAGGAGTATGAGCCCAAGTCCACTGCCAAATTTCCCTGTCTTCCCATCT
1 CTATTGTCACTACATTAAGGAGTATGAGCCCAAGTCCACTGCCAAATTTCCCTGTCTTCCCATCT
*
32041704 ATCTTCCAACCAATGCCCTCATCCTCTGACCAACCTACTCTTAATGGTAGGCCTCAACACGTCCC
66 ATCTTCCAACCAATGCCCTCATCCTCCGACCAACCTACTCTTAATGGTAGGCCTCAACACGTCCC
* * *
32041769 CTCTCTAACGAGAATCCACATTTCAGATGACGAGGAGCACGAGAGGCAATCTAATGCTATGGAGG
131 CTCTCCAACGAGAATCCACATTTCAAATGACGAGAAGCACGAGAGGCAATCTAATGCTATGGAGG
*
32041834 ATTGCTACAGAACTATAGCCAGCTTATTCGAAGAAGAGTTCTCAAACAGCCTTGGGGCTAATATG
196 ATTGCTACAGAACTATAGCCAGCTTATTCGAAGAAGAGTTCTCAAACAGCCTTAGGGCTAATATG
* *
32041899 GTAGAACGGGCAGCTATGGTTGAAAAGGTGCATACCCCAGTTGTATCTATGGGTGTGGATACAAA
261 GTAGAACGGGCAGCTATAGTTGAAAAGATGCATACCCCAGTTGTATCTATGGGTGTGGATACAAA
32041964 AGAAGGTGCC
Statistics
Matches: 301, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
335 301 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.26
Consensus pattern (335 bp):
CTATTGTCACTACATTAAGGAGTATGAGCCCAAGTCCACTGCCAAATTTCCCTGTCTTCCCATCT
ATCTTCCAACCAATGCCCTCATCCTCCGACCAACCTACTCTTAATGGTAGGCCTCAACACGTCCC
CTCTCCAACGAGAATCCACATTTCAAATGACGAGAAGCACGAGAGGCAATCTAATGCTATGGAGG
ATTGCTACAGAACTATAGCCAGCTTATTCGAAGAAGAGTTCTCAAACAGCCTTAGGGCTAATATG
GTAGAACGGGCAGCTATAGTTGAAAAGATGCATACCCCAGTTGTATCTATGGGTGTGGATACAAA
GGAAAGCACG
Found at i:32042056 original size:16 final size:17
Alignment explanation
Indices: 32042023--32042061 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
32042013 GAAGCACAAC
*
32042023 AAGAAGAAGGCCATGAG
1 AAGAAGAAGGCAATGAG
32042040 AAGAAGAAGG-AATGAG
1 AAGAAGAAGGCAATGAG
32042056 AAGAAG
1 AAGAAG
32042062 GTGACTTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.54, C:0.05, G:0.36, T:0.05
Consensus pattern (17 bp):
AAGAAGAAGGCAATGAG
Found at i:32042391 original size:21 final size:21
Alignment explanation
Indices: 32042365--32042405 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
32042355 ATTCGAAGGA
32042365 AAGAAG-AGAAAGCACAAAGAT
1 AAGAAGAAG-AAGCACAAAGAT
*
32042386 AAGAAGAAGAAGCGCAAAGA
1 AAGAAGAAGAAGCACAAAGA
32042406 AGAAAGCGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.61, C:0.10, G:0.27, T:0.02
Consensus pattern (21 bp):
AAGAAGAAGAAGCACAAAGAT
Found at i:32042554 original size:17 final size:18
Alignment explanation
Indices: 32042520--32042558 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
32042510 TTTTATTTAG
*
32042520 TTGTCATTGCATTTTCAT
1 TTGTCACTGCATTTTCAT
32042538 TTGTCACTGCA-TTTCAT
1 TTGTCACTGCATTTTCAT
32042555 TTGT
1 TTGT
32042559 TAGTACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.15, C:0.18, G:0.13, T:0.54
Consensus pattern (18 bp):
TTGTCACTGCATTTTCAT
Found at i:32055663 original size:24 final size:23
Alignment explanation
Indices: 32055630--32055699 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 23
32055620 TAATCTTTTA
*
32055630 AAAATTATAAAGATATAATTTATT
1 AAAATAATAAA-ATATAATTTATT
*
32055654 AAAATAATAAAATTATATTTTTATT
1 AAAATAATAAAA-TATA-ATTTATT
**
32055679 ATCATAA-AAATATATAATTTA
1 AAAATAATAAA-ATATAATTTA
32055700 ATTCTGTTCC
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 5 0.13
24 21 0.55
25 12 0.32
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (23 bp):
AAAATAATAAAATATAATTTATT
Found at i:32058086 original size:18 final size:19
Alignment explanation
Indices: 32058060--32058097 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
32058050 TTGCAAAAAT
*
32058060 AATATAATGGT-TTGTTTA
1 AATAAAATGGTATTGTTTA
*
32058078 AATAAAATGTTATTGTTTA
1 AATAAAATGGTATTGTTTA
32058097 A
1 A
32058098 GAACTTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.47
Consensus pattern (19 bp):
AATAAAATGGTATTGTTTA
Found at i:32058381 original size:23 final size:23
Alignment explanation
Indices: 32058337--32058379 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
32058327 AAATTTTAAA
32058337 TTTTATGAACTTTTTTATTTTAG
1 TTTTATGAACTTTTTTATTTTAG
*
32058360 TTTT-TGAATTTTTTTATTTT
1 TTTTATGAACTTTTTTATTTT
32058380 TAATAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.72
Consensus pattern (23 bp):
TTTTATGAACTTTTTTATTTTAG
Found at i:32068362 original size:21 final size:21
Alignment explanation
Indices: 32068275--32068363 Score: 56
Period size: 21 Copynumber: 4.2 Consensus size: 21
32068265 AGGGAATACC
* *
32068275 AAAAAATATAAGAAAGTACCAAA
1 AAAAAATATGAGGAAGTA-C-AA
* * *
32068298 AAAAAACATGAGGGAGCAC-A
1 AAAAAATATGAGGAAGTACAA
* * * *
32068318 AAAAATTAGGAGGTTA-TACCA
1 AAAAAATATGAGG-AAGTACAA
32068339 AAAAAATATGAGGAAGTACAA
1 AAAAAATATGAGGAAGTACAA
32068360 AAAA
1 AAAA
32068364 TTACGAGGGA
Statistics
Matches: 49, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
20 14 0.29
21 21 0.43
22 1 0.02
23 13 0.27
ACGTcount: A:0.61, C:0.09, G:0.17, T:0.13
Consensus pattern (21 bp):
AAAAAATATGAGGAAGTACAA
Found at i:32068383 original size:41 final size:41
Alignment explanation
Indices: 32068296--32068383 Score: 97
Period size: 41 Copynumber: 2.1 Consensus size: 41
32068286 GAAAGTACCA
* * * *
32068296 AAAAAAAACATGAGGGAGCACAAAAAATTAGGAGGTTATAC
1 AAAAAAAACATGAGGAAGCACAAAAAATTACGAGGTGACAC
* * *
32068337 CAAAAAAATATGAGGAAGTACAAAAAATTACGAGG-GAGCAC
1 AAAAAAAACATGAGGAAGCACAAAAAATTACGAGGTGA-CAC
32068378 AAAAAA
1 AAAAAA
32068384 TTACGAGAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.57, C:0.10, G:0.20, T:0.12
Consensus pattern (41 bp):
AAAAAAAACATGAGGAAGCACAAAAAATTACGAGGTGACAC
Found at i:32068402 original size:61 final size:61
Alignment explanation
Indices: 32068255--32068484 Score: 175
Period size: 61 Copynumber: 3.8 Consensus size: 61
32068245 AGGAAGTATC
** * * * *
32068255 AAAAATTTTGAGGGAATACC-AAAAAATATAAGAAAGTACCAAAAAAAAACATGAGGGAGCACA
1 AAAAATTACGAGGAAATACCAAAAAAATATGAGGAAGTA-CAAAAAATAAC--GAGGGAGCACA
* ** *
32068318 AAAAATTAGGAGGTTATACCAAAAAAATATGAGGAAGTACAAAAAATTACGAGGGAGCACA
1 AAAAATTACGAGGAAATACCAAAAAAATATGAGGAAGTACAAAAAATAACGAGGGAGCACA
* * * * * * *
32068379 AAAAATTACGAGAAAATATC-AAAAATTATGAGAGAA-TACCAAAAATCATG-GGG-GCATACC
1 AAAAATTACGAGGAAATACCAAAAAAATATGAG-GAAGTACAAAAAATAACGAGGGAGC--ACA
* * *
32068439 AAAAAGTATGAGGAAATACCAAAAAAACT-TGAGGAATTACAAAAAA
1 AAAAATTACGAGGAAATACCAAAAAAA-TATGAGGAAGTACAAAAAA
32068485 AATGAGGACA
Statistics
Matches: 136, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
58 2 0.01
59 3 0.02
60 43 0.32
61 46 0.34
62 1 0.01
63 25 0.18
64 16 0.12
ACGTcount: A:0.55, C:0.11, G:0.18, T:0.16
Consensus pattern (61 bp):
AAAAATTACGAGGAAATACCAAAAAAATATGAGGAAGTACAAAAAATAACGAGGGAGCACA
Found at i:32068457 original size:20 final size:20
Alignment explanation
Indices: 32068229--32068463 Score: 107
Period size: 20 Copynumber: 11.6 Consensus size: 20
32068219 AAATTGAAGT
32068229 AATACC-AAAATATATGAGGA
1 AATACCAAAAAT-TATGAGGA
* * * *
32068249 AGTATCAAAAATTTTGAGGG
1 AATACCAAAAATTATGAGGA
* *
32068269 AATACCAAAAAATAT-AAGA
1 AATACCAAAAATTATGAGGA
** *
32068288 AAGTACCAAAAAAAAACATGAGGG
1 AA-TACC---AAAAATTATGAGGA
** * * *
32068312 AGCACAAAAAATTAGGAGGT
1 AATACCAAAAATTATGAGGA
* *
32068332 TATACCAAAAAAATATGAGGA
1 AATACC-AAAAATTATGAGGA
* * * *
32068353 AGTACAAAAAATTACGAGGG
1 AATACCAAAAATTATGAGGA
** * * *
32068373 AGCACAAAAAATTACGAGAA
1 AATACCAAAAATTATGAGGA
*
32068393 AATATCAAAAATTATGA-GA
1 AATACCAAAAATTATGAGGA
* * *
32068412 GAATACCAAAAATCATGGGGG
1 -AATACCAAAAATTATGAGGA
* *
32068433 CATACCAAAAAGTATGAGGA
1 AATACCAAAAATTATGAGGA
32068453 AATACCAAAAA
1 AATACCAAAAA
32068464 AACTTGAGGA
Statistics
Matches: 154, Mismatches: 52, Indels: 18
0.69 0.23 0.08
Matches are distributed among these distances:
19 5 0.03
20 116 0.75
21 20 0.13
23 10 0.06
24 3 0.02
ACGTcount: A:0.54, C:0.11, G:0.18, T:0.17
Consensus pattern (20 bp):
AATACCAAAAATTATGAGGA
Found at i:32068471 original size:21 final size:21
Alignment explanation
Indices: 32068447--32068502 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
32068437 CCAAAAAGTA
*
32068447 TGAGGAAATACCAAAAAAACT
1 TGAGGAAATACAAAAAAAACT
*
32068468 TGAGGAATTACAAAAAAAA--
1 TGAGGAAATACAAAAAAAACT
* *
32068487 TGAGGACATATAAAAA
1 TGAGGAAATACAAAAA
32068503 GAATACGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 13 0.43
21 17 0.57
ACGTcount: A:0.59, C:0.09, G:0.16, T:0.16
Consensus pattern (21 bp):
TGAGGAAATACAAAAAAAACT
Found at i:32068952 original size:40 final size:40
Alignment explanation
Indices: 32068889--32069056 Score: 123
Period size: 40 Copynumber: 4.2 Consensus size: 40
32068879 AGAATACCAA
* * *
32068889 AAAAATATGAGGTAATACT-AAAAACTCTGAAAAAGTACC
1 AAAAATATGAGGAAATACTAAAAAAATATGAAAAAGTACC
* *
32068928 AACAATTATGAGGAAATA-TAAAAAAAATATGAAAAATTACC
1 AA-AAATATGAGGAAATACT-AAAAAAATATGAAAAAGTACC
** * * * *
32068969 AAAAATATGAGGATGT-GTAAAAAATTATTAAAGATGTACC
1 AAAAATATGAGGAAATACTAAAAAAATATGAAA-AAGTACC
** *
32069009 AAAAATTATGAGGGGATAC--AAAAAATATG-AAAATTACC
1 AAAAA-TATGAGGAAATACTAAAAAAATATGAAAAAGTACC
*
32069047 GAAAATATGA
1 AAAAATATGA
32069057 AGATGTACTA
Statistics
Matches: 101, Mismatches: 21, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
37 5 0.05
38 9 0.09
39 17 0.17
40 43 0.43
41 27 0.27
ACGTcount: A:0.55, C:0.08, G:0.14, T:0.23
Consensus pattern (40 bp):
AAAAATATGAGGAAATACTAAAAAAATATGAAAAAGTACC
Found at i:32068992 original size:41 final size:40
Alignment explanation
Indices: 32068916--32069062 Score: 124
Period size: 40 Copynumber: 3.7 Consensus size: 40
32068906 CTAAAAACTC
* * ** *
32068916 TGAAAAAGTACCAACAATTATGAGGAAATATAAAAAAAATA
1 TGAAAAATTACCAA-AAATATGAGGATGTGTAAAAAAAATA
*
32068957 TGAAAAATTACCAAAAATATGAGGATGTGT-AAAAAATTA
1 TGAAAAATTACCAAAAATATGAGGATGTGTAAAAAAAATA
* * *
32068996 TTAAAGATGTACCAAAAATTATGAGG--G-GATACAAAAAATA
1 TGAAAAAT-TACCAAAAA-TATGAGGATGTG-TAAAAAAAATA
* *
32069036 TG-AAAATTACCGAAAATATGAAGATGT
1 TGAAAAATTACCAAAAATATGAGGATGT
32069063 ACTAGAAATT
Statistics
Matches: 85, Mismatches: 14, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
37 6 0.07
38 9 0.11
39 21 0.25
40 29 0.34
41 20 0.24
ACGTcount: A:0.54, C:0.07, G:0.16, T:0.23
Consensus pattern (40 bp):
TGAAAAATTACCAAAAATATGAGGATGTGTAAAAAAAATA
Found at i:32069070 original size:20 final size:18
Alignment explanation
Indices: 32069025--32069076 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
32069015 TATGAGGGGA
*
32069025 TACAAAAAATATGAAAAT
1 TACAGAAAATATGAAAAT
* *
32069043 TACCGAAAATATGAAGAT
1 TACAGAAAATATGAAAAT
*
32069061 GTACTAGAAATTATGA
1 -TAC-AGAAAATATGA
32069077 GGATATATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 15 0.56
19 3 0.11
20 9 0.33
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.25
Consensus pattern (18 bp):
TACAGAAAATATGAAAAT
Found at i:32069072 original size:78 final size:76
Alignment explanation
Indices: 32068931--32069167 Score: 194
Period size: 78 Copynumber: 3.0 Consensus size: 76
32068921 AAGTACCAAC
* * * *
32068931 AATTATGAGGAAATATAAAAAAAATATGAAAAATTACCAAAAATATGAGGATGTGTAAAAAATTA
1 AATTATGA-GAGA-ATACAAAAAATATG-AAAATTACCAAAAATATGAAGATGTCTAAAAAATTA
*
32068996 TTAAAGATGTACCAAA
63 -TAAAGATATA-CAAA
* * * * *
32069012 AATTATGAGGGGATACAAAAAATATGAAAATTACCGAAAATATGAAGATGTACT-AGAAATTATG
1 AATTATGAGAGAATACAAAAAATATGAAAATTACCAAAAATATGAAGATGT-CTAAAAAATTATA
* *
32069076 AGGATATATAAA
65 AAGATATACAAA
* * * * *
32069088 AATTATGAGAGAATACAAAAAAAATGAGAAAATATCAAAAATTCTG-AGAAAGTAC-AAAAAATT
1 AATTATGAGAGAATACAAAAAATATGA-AAATTACCAAAAA-TATGAAG-ATGT-CTAAAAAATT
32069151 ATGAAAGA-ATACAAA
62 AT-AAAGATATACAAA
32069166 AA
1 AA
32069168 AAGTAAGAGA
Statistics
Matches: 126, Mismatches: 24, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
76 27 0.21
77 19 0.15
78 54 0.43
79 17 0.13
80 1 0.01
81 8 0.06
ACGTcount: A:0.57, C:0.05, G:0.15, T:0.23
Consensus pattern (76 bp):
AATTATGAGAGAATACAAAAAATATGAAAATTACCAAAAATATGAAGATGTCTAAAAAATTATAA
AGATATACAAA
Found at i:32069107 original size:19 final size:19
Alignment explanation
Indices: 32069008--32069167 Score: 98
Period size: 19 Copynumber: 8.3 Consensus size: 19
32068998 AAAGATGTAC
* *
32069008 CAAAAATTATGAGGGGATA
1 CAAAAATTATGAGAGAATA
*
32069027 CAAAAAATATGA-A-AATTA
1 CAAAAATTATGAGAGAA-TA
* *
32069045 CCGAAAA-TATGA-AGATGTA
1 -CAAAAATTATGAGAGA-ATA
*
32069064 CTAGAAATTATGAG-GATATA
1 C-AAAAATTATGAGAGA-ATA
*
32069084 TAAAAATTATGAGAGAATA
1 CAAAAATTATGAGAGAATA
** *
32069103 CAAAAAAAATGAGAAAATA
1 CAAAAATTATGAGAGAATA
*
32069122 TCAAAAATTCTGAGA-AAGTA
1 -CAAAAATTATGAGAGAA-TA
*
32069142 CAAAAAATTATGAAAGAATA
1 C-AAAAATTATGAGAGAATA
32069162 CAAAAA
1 CAAAAA
32069168 AAGTAAGAGA
Statistics
Matches: 110, Mismatches: 19, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
17 1 0.01
18 9 0.08
19 59 0.54
20 39 0.35
21 2 0.02
ACGTcount: A:0.57, C:0.06, G:0.15, T:0.21
Consensus pattern (19 bp):
CAAAAATTATGAGAGAATA
Found at i:32069166 original size:39 final size:39
Alignment explanation
Indices: 32068987--32069167 Score: 117
Period size: 39 Copynumber: 4.6 Consensus size: 39
32068977 GAGGATGTGT
* * * *
32068987 AAAAAATTATTAAAGATGTACCAAAAATTATGAGGGGATAC
1 AAAAAATTATGAAAGA-ATA-CAAAAATTATGAGAGAATAC
* * *
32069028 AAAAAA-TATGAAA-ATTACCGAAAA-TATGA-AGATGTAC
1 AAAAAATTATGAAAGAATA-CAAAAATTATGAGAGA-ATAC
* * * *
32069065 TAGAAATTATG-AGGATATATAAAAATTATGAGAGAATAC
1 AAAAAATTATGAAAGA-ATACAAAAATTATGAGAGAATAC
* *
32069104 AAAAAA-AATGAGAA-AATATCAAAAATTCTGAGA-AAGTAC
1 AAAAAATTATGA-AAGAATA-CAAAAATTATGAGAGAA-TAC
32069143 AAAAAATTATGAAAGAATACAAAAA
1 AAAAAATTATGAAAGAATACAAAAA
32069168 AAGTAAGAGA
Statistics
Matches: 108, Mismatches: 20, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
36 1 0.01
37 13 0.12
38 25 0.23
39 45 0.42
40 18 0.17
41 6 0.06
ACGTcount: A:0.57, C:0.06, G:0.14, T:0.22
Consensus pattern (39 bp):
AAAAAATTATGAAAGAATACAAAAATTATGAGAGAATAC
Found at i:32069168 original size:20 final size:20
Alignment explanation
Indices: 32068987--32069168 Score: 78
Period size: 20 Copynumber: 9.3 Consensus size: 20
32068977 GAGGATGTGT
* *
32068987 AAAAAATTATTAAAGATGTAC
1 AAAAAATTATGAAAGA-ATAC
* ** *
32069008 CAAAAATTATGAGGGGATAC
1 AAAAAATTATGAAAGAATAC
*
32069028 AAAAAA-TATGAAA-ATTAC
1 AAAAAATTATGAAAGAATAC
** *
32069046 CGAAAA-TATG-AAGATGTAC
1 AAAAAATTATGAAAGA-ATAC
* * *
32069065 TAGAAATTATG-AGGATATA-
1 AAAAAATTATGAAAGA-ATAC
* *
32069084 TAAAAATTATGAGAGAATAC
1 AAAAAATTATGAAAGAATAC
*
32069104 AAAAAA-AATGAGAA-AATATC
1 AAAAAATTATGA-AAGAATA-C
* *
32069124 -AAAAATTCTGAGAA-AGTAC
1 AAAAAATTATGA-AAGAATAC
32069143 AAAAAATTATGAAAGAATAC
1 AAAAAATTATGAAAGAATAC
32069163 AAAAAA
1 AAAAAA
32069169 AGTAAGAGAA
Statistics
Matches: 121, Mismatches: 30, Indels: 21
0.70 0.17 0.12
Matches are distributed among these distances:
17 2 0.02
18 12 0.10
19 40 0.33
20 56 0.46
21 11 0.09
ACGTcount: A:0.58, C:0.06, G:0.14, T:0.22
Consensus pattern (20 bp):
AAAAAATTATGAAAGAATAC
Found at i:32071437 original size:28 final size:24
Alignment explanation
Indices: 32071356--32071430 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
32071346 AGAAATAATC
* * *
32071356 TTTCAGTTAAACTCTACTTAATTG
1 TTTCAATTAAACTCTATTTATTTG
32071380 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
*
32071404 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
32071428 TTT
1 TTT
32071431 GAGTCAAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:32071439 original size:24 final size:24
Alignment explanation
Indices: 32071364--32071442 Score: 95
Period size: 24 Copynumber: 3.3 Consensus size: 24
32071354 TCTTTCAGTT
* * *
32071364 AAACTCTACTTAATTGTTTCAATT
1 AAACTCTATTTATTTGTTTCAATC
*
32071388 AAACTCTATTTATTTGTTTCAATT
1 AAACTCTATTTATTTGTTTCAATC
* * *
32071412 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTATTTATTTGTTTCAATC
32071436 AAACTCT
1 AAACTCT
32071443 TATTAGTCTA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (24 bp):
AAACTCTATTTATTTGTTTCAATC
Found at i:32072090 original size:20 final size:20
Alignment explanation
Indices: 32071988--32072160 Score: 65
Period size: 20 Copynumber: 8.8 Consensus size: 20
32071978 AAACAATTTC
* * *
32071988 AAAAATTATGTGAAAATACC
1 AAAAATTATGAGGAAATACA
*
32072008 AAGAATT-TGAGGAAATACCA
1 AAAAATTATGAGGAAATA-CA
** * *
32072028 AAACTTTTTAAGGAAA-ACA
1 AAAAATTATGAGGAAATACA
* *
32072047 AAAAA-TATTAGGAAGTATC-
1 AAAAATTATGAGGAAATA-CA
*
32072066 GAAAATTATGAGGAAATACA
1 AAAAATTATGAGGAAATACA
* * **
32072086 AAAAACTCA-AATAAAATATCA
1 AAAAA-TTATGAGGAAATA-CA
* *
32072107 AAAAATT-TGAGAAAATACC
1 AAAAATTATGAGGAAATACA
* *
32072126 AAAAA-TACT-AGGATATACC
1 AAAAATTA-TGAGGAAATACA
32072145 AAAAATTATGACGGAA
1 AAAAATTATGA-GGAA
32072161 TACCCAAAAA
Statistics
Matches: 111, Mismatches: 28, Indels: 27
0.67 0.17 0.16
Matches are distributed among these distances:
18 8 0.07
19 39 0.35
20 45 0.41
21 19 0.17
ACGTcount: A:0.55, C:0.10, G:0.13, T:0.22
Consensus pattern (20 bp):
AAAAATTATGAGGAAATACA
Found at i:32072163 original size:39 final size:38
Alignment explanation
Indices: 32072120--32072208 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 38
32072110 AATTTGAGAA
* * *
32072120 AATACCAAAAATACTAGGATA-TACCAAAAATTATGACGG
1 AATACCAAAAATA-TACGAAAGTACC-AAAATTATAACGG
* *
32072159 AATACCCAAAAATATACGAAAGTACCAAATTTATAAGGG
1 AATA-CCAAAAATATACGAAAGTACCAAAATTATAACGG
32072198 AATACCAAAAA
1 AATACCAAAAA
32072209 AACATGAAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
38 7 0.16
39 23 0.53
40 13 0.30
ACGTcount: A:0.54, C:0.16, G:0.11, T:0.19
Consensus pattern (38 bp):
AATACCAAAAATATACGAAAGTACCAAAATTATAACGG
Found at i:32072551 original size:42 final size:42
Alignment explanation
Indices: 32072505--32072618 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 42
32072495 CCCGAGAAAG
* * * *
32072505 TACCATAAAAAATATGAGGCAATATAAAATATTGTGA-TGGA-A
1 TACCA-AAAAAATATGAGGAAATACAAAAAATTATGAGT-GATA
32072547 TACC-AAAAAATATGAGGAAATACAAAAAATTATGAGTGATA
1 TACCAAAAAAATATGAGGAAATACAAAAAATTATGAGTGATA
* *
32072588 TACCAAAAAAATATGAGGAAGTACCAAAAAT
1 TACCAAAAAAATATGAGGAAATACAAAAAAT
32072619 ATATAAGCAA
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
40 29 0.46
41 6 0.10
42 28 0.44
ACGTcount: A:0.54, C:0.09, G:0.15, T:0.22
Consensus pattern (42 bp):
TACCAAAAAAATATGAGGAAATACAAAAAATTATGAGTGATA
Found at i:32072574 original size:20 final size:20
Alignment explanation
Indices: 32072511--32072720 Score: 115
Period size: 20 Copynumber: 10.3 Consensus size: 20
32072501 AAAGTACCAT
* *
32072511 AAAAAATATGAGGCAATATA
1 AAAAAATATGAGGAAATACA
* * * *
32072531 AAATATTGTGATGG-AATACC
1 AAAAAATATGA-GGAAATACA
32072551 AAAAAATATGAGGAAATACA
1 AAAAAATATGAGGAAATACA
* *
32072571 AAAAATTATGAGTGATATACCA
1 AAAAAATATGAG-GAAATA-CA
*
32072593 AAAAAATATGAGGAAGTACCA
1 AAAAAATATGAGGAAATA-CA
* * *
32072614 AAAATATAT-AAGCAATACA
1 AAAAAATATGAGGAAATACA
32072633 AAAAACA-ATGATGG-AATACCA
1 AAAAA-ATATGA-GGAAATA-CA
** * *
32072654 AAAAAATGCGAGAAAATATA
1 AAAAAATATGAGGAAATACA
* *
32072674 AAAAATTATGAGAAAAATAC-
1 AAAAAATATGAG-GAAATACA
* * *
32072694 CAAAAATATGAGCAAGTACCA
1 AAAAAATATGAGGAAATA-CA
32072715 AAAAAA
1 AAAAAA
32072721 AAATATAAGA
Statistics
Matches: 144, Mismatches: 33, Indels: 25
0.71 0.16 0.12
Matches are distributed among these distances:
19 14 0.10
20 70 0.49
21 47 0.33
22 13 0.09
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.19
Consensus pattern (20 bp):
AAAAAATATGAGGAAATACA
Found at i:32072723 original size:24 final size:24
Alignment explanation
Indices: 32072695--32072742 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
32072685 GAAAAATACC
*
32072695 AAAAATATGAGCA-AGTACCAAAAA
1 AAAAATATAAG-ATAGTACCAAAAA
32072719 AAAAATATAAGATAGTACCAAAAA
1 AAAAATATAAGATAGTACCAAAAA
32072743 TTATGATGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.15
Consensus pattern (24 bp):
AAAAATATAAGATAGTACCAAAAA
Found at i:32074292 original size:31 final size:31
Alignment explanation
Indices: 32074244--32074323 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 31
32074234 ATGGTGCTGC
* * * ***
32074244 CTGACAACAGCCTTCCTCCCCTAGGTGTTGT
1 CTGACAAAAGCCCTCCTCCCCTAGATGCCAT
*
32074275 CTGACAAAAGCCCTCCTCCCTTAGATGCCAT
1 CTGACAAAAGCCCTCCTCCCCTAGATGCCAT
*
32074306 TTGACAAAAGCCCTCCTC
1 CTGACAAAAGCCCTCCTC
32074324 TCATTAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.23, C:0.38, G:0.15, T:0.25
Consensus pattern (31 bp):
CTGACAAAAGCCCTCCTCCCCTAGATGCCAT
Found at i:32076652 original size:102 final size:102
Alignment explanation
Indices: 32076471--32076663 Score: 350
Period size: 102 Copynumber: 1.9 Consensus size: 102
32076461 TCCAGATCCC
*
32076471 TGGTGAAACGGAACTTAATCTTGAATTTGTAAGTGGAAAAATCTGGATCTGTCGTTGAGTTGGTG
1 TGGTAAAACGGAACTTAATCTTGAATTTGTAAGTGGAAAAATCTGGATCTGTCGTTGAGTTGGTG
32076536 AAGATCAAATTAAGTCGTGATTTATTAGTGAAAAATT
66 AAGATCAAATTAAGTCGTGATTTATTAGTGAAAAATT
* * *
32076573 TGGTAAAACGGAACTTCATCTTGAATTTGTAAGTGGAAAATTCTGGATCTGTCTTTGAGTTGGTG
1 TGGTAAAACGGAACTTAATCTTGAATTTGTAAGTGGAAAAATCTGGATCTGTCGTTGAGTTGGTG
32076638 AAGATCAAATTAAGTCGTGATTTATT
66 AAGATCAAATTAAGTCGTGATTTATT
32076664 GATTTAATTG
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 87 1.00
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.36
Consensus pattern (102 bp):
TGGTAAAACGGAACTTAATCTTGAATTTGTAAGTGGAAAAATCTGGATCTGTCGTTGAGTTGGTG
AAGATCAAATTAAGTCGTGATTTATTAGTGAAAAATT
Found at i:32080381 original size:22 final size:23
Alignment explanation
Indices: 32080336--32080380 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
32080326 TTATATGATG
*
32080336 TATTCATGTATTTAAATTTGTTT
1 TATTCATGAATTTAAATTTGTTT
32080359 TATTCAT-AATTT-AATTTGTTT
1 TATTCATGAATTTAAATTTGTTT
32080380 T
1 T
32080381 TTAATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 4 0.19
23 7 0.33
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.62
Consensus pattern (23 bp):
TATTCATGAATTTAAATTTGTTT
Found at i:32091062 original size:41 final size:41
Alignment explanation
Indices: 32091005--32091097 Score: 159
Period size: 41 Copynumber: 2.3 Consensus size: 41
32090995 GAATTTTATT
* * *
32091005 TTAACAAGAATTCTAGTTACTCAATTCTAACAATCTCCACC
1 TTAACAAGAATCCTAGTCACCCAATTCTAACAATCTCCACC
32091046 TTAACAAGAATCCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATCCTAGTCACCCAATTCTAACAATCTCCACC
32091087 TTAACAAGAAT
1 TTAACAAGAAT
32091098 TCTCTACGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.39, C:0.28, G:0.05, T:0.28
Consensus pattern (41 bp):
TTAACAAGAATCCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:32091111 original size:17 final size:17
Alignment explanation
Indices: 32091089--32091128 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
32091079 TCTCCACCTT
* *
32091089 AACAAGAATTCTCTACG
1 AACAAGAACTCTCAACG
*
32091106 AACAAGAACTCTCAATG
1 AACAAGAACTCTCAACG
32091123 AACAAG
1 AACAAG
32091129 TTCTTCACCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.23, G:0.12, T:0.17
Consensus pattern (17 bp):
AACAAGAACTCTCAACG
Found at i:32096218 original size:4 final size:4
Alignment explanation
Indices: 32096209--32096234 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
32096199 TCTATTTCTT
32096209 CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CA
32096235 AATATATGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:32105206 original size:18 final size:18
Alignment explanation
Indices: 32105183--32105217 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
32105173 AATCGAGTTG
*
32105183 ACTCGAATAATTCGATTA
1 ACTCGAATAACTCGATTA
32105201 ACTCGAATAACTCGATT
1 ACTCGAATAACTCGATT
32105218 CGTTTAACTC
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:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (18 bp):
ACTCGAATAACTCGATTA
Found at i:32106392 original size:24 final size:24
Alignment explanation
Indices: 32106375--32106423 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
32106365 TTATATGAAA
32106375 TTTTATTGATTTATTTATTGAGAAT
1 TTTTATTGATTT-TTTATTGAGAAT
* *
32106400 TTTTATTTATTTTTTAAT-AGAAT
1 TTTTATTGATTTTTTATTGAGAAT
32106423 T
1 T
32106424 AGTATTGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.27
24 5 0.23
25 11 0.50
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (24 bp):
TTTTATTGATTTTTTATTGAGAAT
Found at i:32109230 original size:43 final size:44
Alignment explanation
Indices: 32109146--32109231 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 44
32109136 GATGATGAAA
** *
32109146 TTAAATTATTATGTTTGTTCCAAGTTTATTTTAATACATCTAAT
1 TTAAATTACAATGTTTGTTCAAAGTTTATTTTAATACATCTAAT
*
32109190 TTAAATTACAATGTTTGTT-AAAGTTTATTTTAATATATCTAA
1 TTAAATTACAATGTTTGTTCAAAGTTTATTTTAATACATCTAA
32109232 ACCCTATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
43 21 0.55
44 17 0.45
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (44 bp):
TTAAATTACAATGTTTGTTCAAAGTTTATTTTAATACATCTAAT
Found at i:32109319 original size:14 final size:14
Alignment explanation
Indices: 32109283--32109322 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
32109273 ATAAATATTA
*
32109283 AACCCAAAACCCTT
1 AACCCCAAACCCTT
**
32109297 AACAACAAACCCTT
1 AACCCCAAACCCTT
32109311 AACCCCAAACCC
1 AACCCCAAACCC
32109323 CAAGTTGTGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.45, C:0.45, G:0.00, T:0.10
Consensus pattern (14 bp):
AACCCCAAACCCTT
Found at i:32111270 original size:150 final size:144
Alignment explanation
Indices: 32111104--32111497 Score: 456
Period size: 150 Copynumber: 2.7 Consensus size: 144
32111094 ATAATTTCTA
** *
32111104 ATAATTAATTACTAACAAAATGAA-AGTAAATTAAATTAAAAACAACAAAACAATTTATCTTACT
1 ATAA-TAATTACTAACAAAAT-AACTTTAAATTAAATTAAAAACAACAAAACAATTTACCTT-CT
* *
32111168 TTCCTTTCTTTCCATTTAATCTACTCTACTAAATAAAAAATAATAATAACAAATAACATAAAAAT
63 TTACTTTCTTTCC-TTTAATCTACTCTACTAAACAAAAAA-AATAATAACAAATAACATAAAAAT
32111233 TAAACAAAATAACTAAACAAGT
126 TAAACAAAATAA--AAA-AAGT
* *
32111255 ATGATAATTACTAACAAAATAACTTTAAATTAAATTAAAAACAACAAAACAATTTACCTTTCTTA
1 ATAATAATTACTAACAAAATAACTTTAAATTAAATTAAAAACAACAAAACAATTTACC-TTCTTT
* * * *
32111320 AATTTC-TTCTCTTTAATCTACTCTACTAAACAAAAAAAATTATAACAAATCACATAAACATTAA
65 ACTTTCTTTC-CTTTAATCTACTCTACTAAACAAAAAAAATAATAACAAATAACATAAAAATTAA
* * **
32111384 ACTAAATAAATAATTT
129 ACAAAATAAAAAAAGT
*
32111400 ATAATAATTACTAACAAAATAACTTTAATTTAAATT-AAAACAACAACAA-AATTTACCTCTCTT
1 ATAATAATTACTAACAAAATAACTTTAAATTAAATTAAAAACAACAA-AACAATTTACCT-TC-T
* *
32111463 TTGGCTTT-TTTCCTTTTAATCTACTCCACTAAACA
63 TT-ACTTTCTTTCC-TTTAATCTACTCTACTAAACA
32111498 TTAAACTAAA
Statistics
Matches: 213, Mismatches: 21, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
143 1 0.00
144 20 0.09
145 41 0.19
146 28 0.13
148 32 0.15
149 30 0.14
150 56 0.26
151 5 0.02
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (144 bp):
ATAATAATTACTAACAAAATAACTTTAAATTAAATTAAAAACAACAAAACAATTTACCTTCTTTA
CTTTCTTTCCTTTAATCTACTCTACTAAACAAAAAAAATAATAACAAATAACATAAAAATTAAAC
AAAATAAAAAAAGT
Found at i:32111678 original size:15 final size:15
Alignment explanation
Indices: 32111658--32111692 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
32111648 ACTAAACTTT
32111658 ATAAAATAATTAAAA
1 ATAAAATAATTAAAA
*
32111673 ATAAAATAATTTAAA
1 ATAAAATAATTAAAA
32111688 ATAAA
1 ATAAA
32111693 TTAAAACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAAAATAATTAAAA
Found at i:32119783 original size:29 final size:29
Alignment explanation
Indices: 32119674--32119795 Score: 92
Period size: 28 Copynumber: 4.3 Consensus size: 29
32119664 CTAGAAATAA
* *
32119674 CCACAAAAGCTTTCCTTT--TAGAGTTTTT
1 CCACAAAGGTTTTCCTTTAATAG-GTTTTT
* **
32119702 CCACAAAGGTTGTCCTTTAATAGG-TTAG
1 CCACAAAGGTTTTCCTTTAATAGGTTTTT
* * * *
32119730 CTACAAAGGCTTACCTTTTCA-AGGTTTTT
1 CCACAAAGGTTTTCC-TTTAATAGGTTTTT
* *
32119759 CCATAAAGGTTTTCCTTTAATAGG-TTTG
1 CCACAAAGGTTTTCCTTTAATAGGTTTTT
32119787 CCACAAAGG
1 CCACAAAGG
32119796 CATACCTTTT
Statistics
Matches: 70, Mismatches: 19, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
28 46 0.66
29 21 0.30
30 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (29 bp):
CCACAAAGGTTTTCCTTTAATAGGTTTTT
Found at i:32119842 original size:58 final size:58
Alignment explanation
Indices: 32119674--32119887 Score: 267
Period size: 57 Copynumber: 3.8 Consensus size: 58
32119664 CTAGAAATAA
* * *
32119674 CCACAAAAGCTTTCCTTTT--AGAGTTTTTCCACAAAGGTTGTCCTTTAATAGGTTAG
1 CCACAAAGGCTTACCTTTTCAAGAGTTTTTCCATAAAGGTTGTCCTTTAATAGGTTAG
* * *
32119730 CTACAAAGGCTTACCTTTTCAAG-GTTTTTCCATAAAGGTTTTCCTTTAATAGGTTTG
1 CCACAAAGGCTTACCTTTTCAAGAGTTTTTCCATAAAGGTTGTCCTTTAATAGGTTAG
* * * * *
32119787 CCACAAAGGCATACCTTTTCCAGAGTTTTGT-CGTAAAGGTTGTCCTTTAACAGGTTCG
1 CCACAAAGGCTTACCTTTTCAAGAGTTTT-TCCATAAAGGTTGTCCTTTAATAGGTTAG
* *
32119845 CCAAAAAGGCTTACC-TTTCTAGAGTTTTTCCATAAAGGTTGTC
1 CCACAAAGGCTTACCTTTTCAAGAGTTTTTCCATAAAGGTTGTC
32119888 ATTTCTTAGT
Statistics
Matches: 136, Mismatches: 17, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
56 17 0.12
57 75 0.55
58 43 0.32
59 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (58 bp):
CCACAAAGGCTTACCTTTTCAAGAGTTTTTCCATAAAGGTTGTCCTTTAATAGGTTAG
Found at i:32122734 original size:21 final size:23
Alignment explanation
Indices: 32122710--32122754 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
32122700 CCTGTCATTT
*
32122710 ATTAAAT-AAATG-ATCTAGAAA
1 ATTAAATAAAACGTATCTAGAAA
32122731 ATTAAATAAAACGTATCTAGAAA
1 ATTAAATAAAACGTATCTAGAAA
32122754 A
1 A
32122755 CAACCCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 4 0.19
23 10 0.48
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.27
Consensus pattern (23 bp):
ATTAAATAAAACGTATCTAGAAA
Found at i:32124148 original size:9 final size:9
Alignment explanation
Indices: 32124134--32124161 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
32124124 TTTTATTTTT
32124134 AAAATATTA
1 AAAATATTA
32124143 AAAATATTA
1 AAAATATTA
32124152 AAAATATTA
1 AAAATATTA
32124161 A
1 A
32124162 TATAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATATTA
Found at i:32124290 original size:13 final size:14
Alignment explanation
Indices: 32124273--32124317 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
32124263 ATTTCAATTT
32124273 TATTTTAATAATAA
1 TATTTTAATAATAA
* *
32124287 -ATTTTAAAAAAAA
1 TATTTTAATAATAA
32124300 TATTTT-A-AATAA
1 TATTTTAATAATAA
32124312 TATTTT
1 TATTTT
32124318 CACATATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 10 0.37
13 12 0.44
14 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATTTTAATAATAA
Done.