Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 139 of 193
Found at i:43567810 original size:39 final size:39
Alignment explanation
Indices: 43567767--43568026 Score: 367
Period size: 39 Copynumber: 6.7 Consensus size: 39
43567757 CATTACGGTA
* * *
43567767 TTTACAGTGTTACTGCCAGTTTAGTATTGTATTGTAGTG
1 TTTACAGTGTCACTGTCAGTTCAGTATTGTATTGTAGTG
* *
43567806 TTTACAGTGTCACTGTCGGTTCAGTATTGTATTGTAATG
1 TTTACAGTGTCACTGTCAGTTCAGTATTGTATTGTAGTG
** *
43567845 TTTACAGTGTCACTACCAGTTCAGTATTGTACTGTAGTG
1 TTTACAGTGTCACTGTCAGTTCAGTATTGTATTGTAGTG
* *
43567884 TTTACAGTGTCACTGCCAGTTCAGTATTGTATTATAGTG
1 TTTACAGTGTCACTGTCAGTTCAGTATTGTATTGTAGTG
* * *
43567923 TTTACACTGTCACAGTCAGTTCAATATTGTATTGTAGTG
1 TTTACAGTGTCACTGTCAGTTCAGTATTGTATTGTAGTG
* * * *
43567962 TTTACAATGTCACTGTCAGATCAGTATTATATTGCAGTG
1 TTTACAGTGTCACTGTCAGTTCAGTATTGTATTGTAGTG
43568001 TTTACAGTGTCACTGTCAGTTCAGTA
1 TTTACAGTGTCACTGTCAGTTCAGTA
43568027 ATTTGATAAC
Statistics
Matches: 195, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 195 1.00
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.41
Consensus pattern (39 bp):
TTTACAGTGTCACTGTCAGTTCAGTATTGTATTGTAGTG
Found at i:43567828 original size:78 final size:78
Alignment explanation
Indices: 43567725--43568026 Score: 361
Period size: 78 Copynumber: 3.9 Consensus size: 78
43567715 TAGCATTACG
* ** * * * ** * * *
43567725 GTGTTTACAGTATCACCATCAGTTCAATACTGCATTACGGTATTTACAGTGTTACTGCCAGTTTA
1 GTGTTTACAGTGTCACTGTCAGTTCAGTATTGTATTATAGTGTTTACAGTGTCACTGCCAGTTCA
43567790 GTATTGTATTGTA
66 GTATTGTATTGTA
* * * *
43567803 GTGTTTACAGTGTCACTGTCGGTTCAGTATTGTATTGTAATGTTTACAGTGTCACTACCAGTTCA
1 GTGTTTACAGTGTCACTGTCAGTTCAGTATTGTATTATAGTGTTTACAGTGTCACTGCCAGTTCA
*
43567868 GTATTGTACTGTA
66 GTATTGTATTGTA
* * * *
43567881 GTGTTTACAGTGTCACTGCCAGTTCAGTATTGTATTATAGTGTTTACACTGTCACAGTCAGTTCA
1 GTGTTTACAGTGTCACTGTCAGTTCAGTATTGTATTATAGTGTTTACAGTGTCACTGCCAGTTCA
*
43567946 ATATTGTATTGTA
66 GTATTGTATTGTA
* * * ** *
43567959 GTGTTTACAATGTCACTGTCAGATCAGTATTATATTGCAGTGTTTACAGTGTCACTGTCAGTTCA
1 GTGTTTACAGTGTCACTGTCAGTTCAGTATTGTATTATAGTGTTTACAGTGTCACTGCCAGTTCA
43568024 GTA
66 GTA
43568027 ATTTGATAAC
Statistics
Matches: 189, Mismatches: 35, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
78 189 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (78 bp):
GTGTTTACAGTGTCACTGTCAGTTCAGTATTGTATTATAGTGTTTACAGTGTCACTGCCAGTTCA
GTATTGTATTGTA
Found at i:43573166 original size:4 final size:4
Alignment explanation
Indices: 43573148--43573181 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
43573138 AATTGTCATA
*
43573148 AAAG AAA- AAAA AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
43573182 AAGTTCATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:43573176 original size:12 final size:12
Alignment explanation
Indices: 43573147--43573183 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
43573137 TAATTGTCAT
43573147 AAAAGAAA-AAA
1 AAAAGAAAGAAA
43573158 AAAAGAAAGAAA
1 AAAAGAAAGAAA
*
43573170 GAAAGAAAGAAA
1 AAAAGAAAGAAA
43573182 AA
1 AA
43573184 GTTCATTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAGAAAGAAA
Found at i:43577680 original size:21 final size:21
Alignment explanation
Indices: 43577641--43577680 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
43577631 ATCATTTCAG
*
43577641 TTTTTTTTCTTAATTTCCCTT
1 TTTTTTTTCTTAATCTCCCTT
43577662 TTTTTTTTCTTTAA-CTCCC
1 TTTTTTTTC-TTAATCTCCC
43577681 AGCTTCTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTTTTTCTTAATCTCCCTT
Found at i:43578773 original size:12 final size:12
Alignment explanation
Indices: 43578738--43578775 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
43578728 CAAGACAACC
*
43578738 CATCAACATCAA
1 CATCAACATCAT
43578750 CATCAACATCAT
1 CATCAACATCAT
*
43578762 CATCATCATCAT
1 CATCAACATCAT
43578774 CA
1 CA
43578776 GTTGATGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.42, C:0.34, G:0.00, T:0.24
Consensus pattern (12 bp):
CATCAACATCAT
Found at i:43578775 original size:6 final size:6
Alignment explanation
Indices: 43578738--43578772 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
43578728 CAAGACAACC
* *
43578738 CATCAA CATCAA CATCAA CATCAT CATCAT CATCA
1 CATCAA CATCAA CATCAA CATCAA CATCAA CATCA
43578773 TCAGTTGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.23
Consensus pattern (6 bp):
CATCAA
Found at i:43581258 original size:14 final size:13
Alignment explanation
Indices: 43581232--43581256 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43581222 TTTATGAACT
43581232 TTTTATAATTTTA
1 TTTTATAATTTTA
43581245 TTTTATAATTTT
1 TTTTATAATTTT
43581257 TAAATTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTATAATTTTA
Found at i:43583975 original size:31 final size:31
Alignment explanation
Indices: 43583915--43583976 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
43583905 GTTTTATATC
*
43583915 TTTATAACGTTTTAAAAGATTAAATCAAAAT
1 TTTATAACGTTTTAAAAGATCAAATCAAAAT
*
43583946 TTTATAA-GTTTT-AAGGATCAAAGTACAAAAT
1 TTTATAACGTTTTAAAAGATCAAA-T-CAAAAT
43583977 CACTATATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 8 0.30
30 6 0.22
31 13 0.48
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (31 bp):
TTTATAACGTTTTAAAAGATCAAATCAAAAT
Found at i:43588198 original size:18 final size:17
Alignment explanation
Indices: 43588177--43588219 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
43588167 TAATCTAGTC
43588177 ATAATAATAAAAAAAGAT
1 ATAATAATAAAAAAAG-T
**
43588195 ATAATTTTAAAAAAAGT
1 ATAATAATAAAAAAAGT
*
43588212 TTAATAAT
1 ATAATAAT
43588220 TATAGCATAG
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
ATAATAATAAAAAAAGT
Found at i:43592164 original size:22 final size:22
Alignment explanation
Indices: 43592139--43592188 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
43592129 GAAATTTAAA
*
43592139 ACAAAACATTATGAGGAGAGTT
1 ACAAAACATTATGAGAAGAGTT
43592161 ACAAAACATTATGAGAAGAGTT
1 ACAAAACATTATGAGAAGAGTT
43592183 ACAAAA
1 ACAAAA
43592189 TAATATTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.52, C:0.10, G:0.18, T:0.20
Consensus pattern (22 bp):
ACAAAACATTATGAGAAGAGTT
Found at i:43594231 original size:16 final size:16
Alignment explanation
Indices: 43594210--43594242 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43594200 AATTTTATTA
43594210 TTTTAAAA-ATTATAAT
1 TTTTAAAAGATTA-AAT
43594226 TTTTAAAAGATTAAAT
1 TTTTAAAAGATTAAAT
43594242 T
1 T
43594243 AAATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TTTTAAAAGATTAAAT
Found at i:43594248 original size:44 final size:45
Alignment explanation
Indices: 43594172--43594258 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 45
43594162 AGCTGGAATT
** *
43594172 AAATTATAATTTTTATGATAGTAATTATAA-TTTTATTATTTTAA
1 AAATTATAATTTTTAAAAGAGTAATTATAATTTTTATTATTTTAA
*
43594216 AAATTATAATTTTTAAAAGATTAAATTA-AATTTTTATTATTTT
1 AAATTATAATTTTTAAAAGAGT-AATTATAATTTTTATTATTTT
43594259 TAAGGAGGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 20 0.54
45 17 0.46
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (45 bp):
AAATTATAATTTTTAAAAGAGTAATTATAATTTTTATTATTTTAA
Found at i:43595053 original size:41 final size:41
Alignment explanation
Indices: 43595005--43595083 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
43594995 TTAATTCTTG
* * *
43595005 TTTTAGTACCTTCTAAATGTAAATAGTTCATTTTAATCGAC
1 TTTTAGTACCTTCAAAATATAAATAGATCATTTTAATCGAC
43595046 TTTTAGTACCTTCAAAATATAAATAGATCATTTTAATC
1 TTTTAGTACCTTCAAAATATAAATAGATCATTTTAATC
43595084 TATTTTAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (41 bp):
TTTTAGTACCTTCAAAATATAAATAGATCATTTTAATCGAC
Found at i:43596354 original size:24 final size:24
Alignment explanation
Indices: 43596326--43596371 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
43596316 TAAATTAGAG
*
43596326 GGACTTTAGTGATAATGTAAAGGA
1 GGACTTTACTGATAATGTAAAGGA
43596350 GGACTTTACTGATAATGTAAAG
1 GGACTTTACTGATAATGTAAAG
43596372 AGATTATGGA
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:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (24 bp):
GGACTTTACTGATAATGTAAAGGA
Found at i:43601729 original size:30 final size:31
Alignment explanation
Indices: 43601693--43601754 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
43601683 CAAAAATATA
* *
43601693 AAATTTAGATATATT-GTTTTGAATTTTTAG
1 AAATTTAGATATATTAATTTTGAAATTTTAG
*
43601723 AAATTTAGATATGTTAATTTTGAAATTTTAG
1 AAATTTAGATATATTAATTTTGAAATTTTAG
43601754 A
1 A
43601755 CTTTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (31 bp):
AAATTTAGATATATTAATTTTGAAATTTTAG
Found at i:43612151 original size:3 final size:3
Alignment explanation
Indices: 43612145--43612207 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
43612135 CCATAATTGA
43612145 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
43612193 TAT TAT AAT T-T TAT T
1 TAT TAT TAT TAT TAT T
43612208 TCTTGGGAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:43616946 original size:10 final size:11
Alignment explanation
Indices: 43616919--43616946 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
43616909 TTTCTCTACT
43616919 TCAAAAAGTTG
1 TCAAAAAGTTG
43616930 TCAAAAAGTTG
1 TCAAAAAGTTG
43616941 TCAAAA
1 TCAAAA
43616947 TTATTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (11 bp):
TCAAAAAGTTG
Found at i:43620325 original size:3 final size:3
Alignment explanation
Indices: 43620317--43620346 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
43620307 TTTTAAATCA
43620317 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
43620347 TTGTATGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:43621742 original size:3 final size:3
Alignment explanation
Indices: 43621734--43621758 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
43621724 TTCATATGAA
43621734 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
43621759 GAGCACACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:43622337 original size:30 final size:31
Alignment explanation
Indices: 43622286--43622351 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
43622276 ACTCGGATAC
* *
43622286 CAAAATGAACATTAAAGCTAAAATTATGTA-
1 CAAATTGAACATTAAAGCTAAAATTAAGTAT
* *
43622316 CAAATTGAATATTGAAA-CTAAATTTAAGTAT
1 CAAATTGAACATT-AAAGCTAAAATTAAGTAT
43622347 CAAAT
1 CAAAT
43622352 AGTATATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (31 bp):
CAAATTGAACATTAAAGCTAAAATTAAGTAT
Found at i:43640542 original size:13 final size:14
Alignment explanation
Indices: 43640524--43640556 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
43640514 AAACCCTAAA
43640524 CTTAAAT-TCGAAT
1 CTTAAATCTCGAAT
43640537 CTTAAATCTCGAAT
1 CTTAAATCTCGAAT
*
43640551 TTTAAA
1 CTTAAA
43640557 CTTGAGTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.39
Consensus pattern (14 bp):
CTTAAATCTCGAAT
Found at i:43641941 original size:14 final size:14
Alignment explanation
Indices: 43641922--43641956 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
43641912 AAAACCATTG
43641922 GATCTTTTTTTTTA
1 GATCTTTTTTTTTA
43641936 GATCTTTTTTTTTA
1 GATCTTTTTTTTTA
43641950 GATCTTT
1 GATCTTT
43641957 CAAAGGCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.69
Consensus pattern (14 bp):
GATCTTTTTTTTTA
Found at i:43653341 original size:3 final size:3
Alignment explanation
Indices: 43653333--43653358 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
43653323 CATTTTTAAA
43653333 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
43653359 GCGTTTCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:43659315 original size:20 final size:20
Alignment explanation
Indices: 43659290--43659327 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
43659280 TATGTTTGAA
43659290 ATGTTA-CGTTTTAGTTACTT
1 ATGTTATCGTTTT-GTTACTT
43659310 ATGTTATCGTTTTGTTAC
1 ATGTTATCGTTTTGTTAC
43659328 GAAGTGGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.18, C:0.11, G:0.16, T:0.55
Consensus pattern (20 bp):
ATGTTATCGTTTTGTTACTT
Found at i:43659465 original size:18 final size:18
Alignment explanation
Indices: 43659442--43659484 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
43659432 GAATAAGTTT
43659442 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
43659460 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
43659478 TTAATTA
1 TTAATTA
43659485 CATCTTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:43681734 original size:101 final size:101
Alignment explanation
Indices: 43681618--43681822 Score: 410
Period size: 101 Copynumber: 2.0 Consensus size: 101
43681608 CTTTTTAGTT
43681618 TTTTTATAATTTGTATAAATTTAATAGTCTAACTTTTTACTAATATTTTGATAAAAATACATTAT
1 TTTTTATAATTTGTATAAATTTAATAGTCTAACTTTTTACTAATATTTTGATAAAAATACATTAT
43681683 ATATCACATACAAACGCAAACATTCATATAAATATA
66 ATATCACATACAAACGCAAACATTCATATAAATATA
43681719 TTTTTATAATTTGTATAAATTTAATAGTCTAACTTTTTACTAATATTTTGATAAAAATACATTAT
1 TTTTTATAATTTGTATAAATTTAATAGTCTAACTTTTTACTAATATTTTGATAAAAATACATTAT
43681784 ATATCACATACAAACGCAAACATTCATATAAATATA
66 ATATCACATACAAACGCAAACATTCATATAAATATA
43681820 TTT
1 TTT
43681823 ATATGTAAAT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 104 1.00
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (101 bp):
TTTTTATAATTTGTATAAATTTAATAGTCTAACTTTTTACTAATATTTTGATAAAAATACATTAT
ATATCACATACAAACGCAAACATTCATATAAATATA
Found at i:43681955 original size:20 final size:19
Alignment explanation
Indices: 43681927--43681964 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
43681917 GTTAAGATAA
43681927 AAAATTTAAAAATTGATTT
1 AAAATTTAAAAATTGATTT
*
43681946 AAAATATTAAAATTTGATT
1 AAAAT-TTAAAAATTGATT
43681965 CGAATCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
AAAATTTAAAAATTGATTT
Found at i:43682933 original size:32 final size:32
Alignment explanation
Indices: 43682873--43682939 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 32
43682863 GAAATTTAAA
*
43682873 AAATTCAAAAATAATATAAAAACTATTTTTAT
1 AAATTCAAAAATAATAAAAAAACTATTTTTAT
* * *
43682905 AAATT-AAAAATTATAAAAAAATTAATTTTA-
1 AAATTCAAAAATAATAAAAAAACTATTTTTAT
43682935 AAATT
1 AAATT
43682940 TTAATTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 5 0.16
31 21 0.68
32 5 0.16
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (32 bp):
AAATTCAAAAATAATAAAAAAACTATTTTTAT
Found at i:43684818 original size:23 final size:22
Alignment explanation
Indices: 43684780--43684826 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
43684770 TGTGATGACG
43684780 ATTTCGATGACAATTATGATTATT
1 ATTTCGATGACAATTAT--TTATT
*
43684804 ATTTC-ATGACGATTATTTATT
1 ATTTCGATGACAATTATTTATT
43684825 AT
1 AT
43684827 CATCATTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
23 10 0.45
24 5 0.23
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.49
Consensus pattern (22 bp):
ATTTCGATGACAATTATTTATT
Found at i:43711641 original size:15 final size:15
Alignment explanation
Indices: 43711623--43711652 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
43711613 ATCAAATACA
43711623 AATATAATATATTAT
1 AATATAATATATTAT
43711638 AATATAATATATTAT
1 AATATAATATATTAT
43711653 TTATTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATAATATATTAT
Found at i:43711673 original size:13 final size:13
Alignment explanation
Indices: 43711655--43711680 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43711645 TATATTATTT
43711655 ATTTAATTAATTA
1 ATTTAATTAATTA
43711668 ATTTAATTAATTA
1 ATTTAATTAATTA
43711681 TATTAATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTTAATTAATTA
Found at i:43714160 original size:14 final size:14
Alignment explanation
Indices: 43714141--43714171 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43714131 GAATCTGTAG
43714141 AATGAAAATGATTA
1 AATGAAAATGATTA
*
43714155 AATGAAATTGATTA
1 AATGAAAATGATTA
43714169 AAT
1 AAT
43714172 AGGAATGTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (14 bp):
AATGAAAATGATTA
Found at i:43719055 original size:57 final size:57
Alignment explanation
Indices: 43718967--43719080 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 57
43718957 TTAAGAGAAA
* *
43718967 AAATTTAATTTGTTACTTTTTTATTGAAAAAGAATAGGGATAATATAAAATCACAGT
1 AAATTTAATTTGTTACTTTTTTATTGAAAAAGAATAGAGATAACATAAAATCACAGT
*
43719024 AAATTTAATTTGTTA-TTCTTTTATTGAAAAAGAATAGAGATAACGTAAAATCACAGT
1 AAATTTAATTTGTTACTT-TTTTATTGAAAAAGAATAGAGATAACATAAAATCACAGT
43719081 TTCATACAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
56 2 0.04
57 51 0.96
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (57 bp):
AAATTTAATTTGTTACTTTTTTATTGAAAAAGAATAGAGATAACATAAAATCACAGT
Found at i:43729841 original size:15 final size:17
Alignment explanation
Indices: 43729800--43729834 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
43729790 AAGAAACTAA
43729800 AATATAATTTTACAATT
1 AATATAATTTTACAATT
*
43729817 AATATAATTTTGCAATT
1 AATATAATTTTACAATT
43729834 A
1 A
43729835 TTAATTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (17 bp):
AATATAATTTTACAATT
Found at i:43739338 original size:31 final size:29
Alignment explanation
Indices: 43739283--43739353 Score: 97
Period size: 31 Copynumber: 2.4 Consensus size: 29
43739273 AATGTTTGAA
*
43739283 TTAATTTTAAATTCATTTTTAAATTTATC
1 TTAAATTTAAATTCATTTTTAAATTTATC
* *
43739312 TTAAATTTAAATTTACTTATTTAAATTTATT
1 TTAAATTTAAATTCA-TT-TTTAAATTTATC
43739343 TTAAATTTAAA
1 TTAAATTTAAA
43739354 CCTAATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 13 0.35
30 2 0.05
31 22 0.59
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.56
Consensus pattern (29 bp):
TTAAATTTAAATTCATTTTTAAATTTATC
Found at i:43739350 original size:11 final size:11
Alignment explanation
Indices: 43739281--43739351 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
43739271 TTAATGTTTG
*
43739281 AATTAATTTTA
1 AATTTATTTTA
*
43739292 AATTCATTTTTA
1 AATTTA-TTTTA
*
43739304 AATTTATCTTA
1 AATTTATTTTA
*
43739315 AATTTAAATTT-
1 AATTT-ATTTTA
*
43739326 -ACTTA-TTTA
1 AATTTATTTTA
43739335 AATTTATTTTA
1 AATTTATTTTA
43739346 AATTTA
1 AATTTA
43739352 AACCTAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
8 3 0.06
9 1 0.02
10 7 0.15
11 24 0.50
12 13 0.27
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTATTTTA
Found at i:43739446 original size:17 final size:17
Alignment explanation
Indices: 43739424--43739456 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
43739414 AGCCCAAATT
43739424 AAAGGCCCGATTACAAA
1 AAAGGCCCGATTACAAA
43739441 AAAGGCCCGATTACAA
1 AAAGGCCCGATTACAA
43739457 GAAGCCCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.24, G:0.18, T:0.12
Consensus pattern (17 bp):
AAAGGCCCGATTACAAA
Found at i:43740327 original size:16 final size:15
Alignment explanation
Indices: 43740306--43740336 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
43740296 GGAAACATTT
43740306 CCAGATCTGGGCTTCC
1 CCAGATCTGGG-TTCC
43740322 CCAGATCTGGGTTCC
1 CCAGATCTGGGTTCC
43740337 GAAAAACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.13, C:0.35, G:0.26, T:0.26
Consensus pattern (15 bp):
CCAGATCTGGGTTCC
Found at i:43740378 original size:20 final size:18
Alignment explanation
Indices: 43740349--43740393 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
43740339 AAAACCAAAC
43740349 AAAAAAAATAGA-AAGAAAT
1 AAAAAAAATA-ATAAG-AAT
43740368 AAAAAATAATAATAAGAAT
1 AAAAAA-AATAATAAGAAT
43740387 AAAAAAA
1 AAAAAAA
43740394 GAAGCTTTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 1 0.04
19 16 0.67
20 7 0.29
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (18 bp):
AAAAAAAATAATAAGAAT
Found at i:43741060 original size:160 final size:162
Alignment explanation
Indices: 43740873--43741217 Score: 439
Period size: 160 Copynumber: 2.1 Consensus size: 162
43740863 AATTTTAATT
* **
43740873 GGTTTATAATTTAGTCCTTTGACTGTTTGACTGTGCCAGAGGCTGCCACGTGTC-ATGTTTTGGA
1 GGTTTATAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCAAT-TTTTGGA
* * *
43740937 TTATTTATGAATTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCC-CAAATCAACT-TTA
65 TTATTTATGAATTTAGTCCCTTCTATTTTTAATTTATTTTAATTTAATCCTCAAATCAACTGTTA
** * *
43741000 TTTTAATTATGAAATTAG-CCCAATATTTTTCAA
130 -TTTAATTACAAAATTAGTCCAAAAATTTTTCAA
* * *
43741033 GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCAATTTTTGGCT
1 GGTTTATAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCAATTTTTGGAT
* * * * * *
43741098 TATTTCTGCATTTAGTCCCTTCTATTTTTAATTTATTTTCATTTAGTCCTTAAATTAACTGTTAT
66 TATTTATGAATTTAGTCCCTTCTATTTTTAATTTATTTTAATTTAATCCTCAAATCAACTGTTAT
*
43741163 TTAATTACAAAATTGGTCCAAAAATTTTTCAA
131 TTAATTACAAAATTAGTCCAAAAATTTTTCAA
*
43741195 AGTTT-TCAAATTAGTCCTTTGAC
1 GGTTTAT-AAATTAGTCCTTTGAC
43741218 CTCTGGATAC
Statistics
Matches: 158, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
160 98 0.62
161 25 0.16
162 35 0.22
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (162 bp):
GGTTTATAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCAATTTTTGGAT
TATTTATGAATTTAGTCCCTTCTATTTTTAATTTATTTTAATTTAATCCTCAAATCAACTGTTAT
TTAATTACAAAATTAGTCCAAAAATTTTTCAA
Found at i:43741334 original size:30 final size:30
Alignment explanation
Indices: 43741288--43741366 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
43741278 CCTTAAATTG
* * *
43741288 TCCAGAAATCATATTTTGACCCCAAAACTTT
1 TCCA-AAATTATATTTTAACCACAAAACTTT
*
43741319 TCTAAAATTATATTTTAACCACAAAACTTT
1 TCCAAAATTATATTTTAACCACAAAACTTT
*
43741349 TCCAAAATTACATTTTAA
1 TCCAAAATTATATTTTAA
43741367 GCCCGATTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 39 0.93
31 3 0.07
ACGTcount: A:0.41, C:0.20, G:0.03, T:0.37
Consensus pattern (30 bp):
TCCAAAATTATATTTTAACCACAAAACTTT
Found at i:43741589 original size:58 final size:59
Alignment explanation
Indices: 43741352--43741752 Score: 531
Period size: 59 Copynumber: 6.9 Consensus size: 59
43741342 AAACTTTTCC
* * * * *
43741352 AAAATTACA-TTTTAAGCCCGATTTCACCGAAAATTACAATTTTACCCCCGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAACTTCT
* * *
43741410 AGAATTCCGTTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAAACTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAACTTCT
* * * *
43741469 AAAATTCCGTTTTTAACCCGGATTTCACCGAAAATTACTATTTTACCCTCGAAACTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAACTTCT
* *
43741528 AAAATTCCATTTTTAACCTCGATTTCACC-AAAATTACCATTTTACCCCTGAAACTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAACTTCT
* * **
43741586 AAAATTCCATTTTTAACCCCTATTTCACCGAAAATTACCTTTTTACCCCAAAAACTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAACTTCT
* * * *
43741645 AAAATTCTATTTTTAACCCCGATTTCACCGAAATTTACCATTTTA-CCCCGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAACTTCT
* * ** *
43741703 AAAATTCTATTTTTAACCCCGATTACGTC-AAAATTACCATTTTGCCCCCG
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCG
43741753 GGTATCCATA
Statistics
Matches: 303, Mismatches: 37, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
57 13 0.04
58 99 0.33
59 191 0.63
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAACTTCT
Found at i:43741616 original size:117 final size:116
Alignment explanation
Indices: 43741352--43741726 Score: 513
Period size: 117 Copynumber: 3.2 Consensus size: 116
43741342 AAACTTTTCC
* * * * * *
43741352 AAAATTACA-TTTTAAGCCCGATTTCACCGAAAATTACAATTTTACCCCCGAATCTTTTAGAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACTATTTTA-CCCCGAAACTTCTAAAATT
*
43741416 CCGTTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAAACTTCT
65 CCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTA-CCCCGAAACTTCT
* *
43741469 AAAATTCCGTTTTTAACCCGGATTTCACCGAAAATTACTATTTTACCCTCGAAACTTCTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACTATTTTACCC-CGAAACTTCTAAAATT
*
43741534 CCATTTTTAACCTCGATTTCACC-AAAATTACCATTTTACCCCTGAAACTTCT
65 CCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCC-GAAACTTCT
* *
43741586 AAAATTCCATTTTTAACCCCTATTTCACCGAAAATTACCT-TTTTACCCCAAAAACTTCTAAAAT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTA-CTATTTTACCCC-GAAACTTCTAAAAT
* * * * *
43741650 TCTATTTTTAACCCCGATTTCACCGAAATTTACCATTTTACCCCGAATCTTTT
64 TCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCGAAACTTCT
*
43741703 AAAATTCTATTTTTAACCCCGATT
1 AAAATTCCATTTTTAACCCCGATT
43741727 ACGTCAAAAT
Statistics
Matches: 231, Mismatches: 21, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
116 5 0.02
117 140 0.61
118 86 0.37
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (116 bp):
AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACTATTTTACCCCGAAACTTCTAAAATTC
CATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCGAAACTTCT
Found at i:43756954 original size:31 final size:31
Alignment explanation
Indices: 43756909--43757163 Score: 162
Period size: 31 Copynumber: 7.7 Consensus size: 31
43756899 TAACACATCT
43756909 TCATCT-CT-GAAATTGAAGTAAGAGCAACG
1 TCATCTCCTCGAAATTGAAGTAAGAGCAACG
*
43756938 TCATCTCCTCGAAATTGAAGT-AGAATGGATAAC-
1 TCATCTCCTCGAAATTGAAGTAAG-A--G-CAACG
*
43756971 ACATCTTCATCTCTGAAATTGAAGTAAGAGCAACG
1 TCATC-TC--CTC-GAAATTGAAGTAAGAGCAACG
* *
43757006 TCATCTCCTCGAAATTGAAGTAGAGTGGATAAC-
1 TCATCTCCTCGAAATTGAAGTA-AG-AG-CAACG
* *
43757039 ACATCTTTATCTCTGAAATTGAAGTAAGAGCAACG
1 TCATC--T-CCTC-GAAATTGAAGTAAGAGCAACG
* *
43757074 TCATCTCCTCGAAATTGAAGTAGAGTGGATAAC-
1 TCATCTCCTCGAAATTGAAGTA-AG-AG-CAACG
* *
43757107 ACATCTTTATCTCTGAAATTGAAGTAAGAGCAACG
1 TCATC--T-CCTC-GAAATTGAAGTAAGAGCAACG
* *
43757142 TCATCCCCTTGAAATTGAAGTA
1 TCATCTCCTCGAAATTGAAGTA
43757164 GAGTGGATAA
Statistics
Matches: 176, Mismatches: 22, Indels: 54
0.70 0.09 0.21
Matches are distributed among these distances:
29 6 0.03
30 4 0.02
31 48 0.27
32 12 0.07
33 16 0.09
34 22 0.12
35 17 0.10
36 13 0.07
37 36 0.20
38 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (31 bp):
TCATCTCCTCGAAATTGAAGTAAGAGCAACG
Found at i:43757230 original size:204 final size:204
Alignment explanation
Indices: 43756866--43757374 Score: 740
Period size: 204 Copynumber: 2.6 Consensus size: 204
43756856 TGCAGGTCTT
43756866 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTCATCTCTGAAATTGAAGTAAG
1 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTCATCTCTGAAATTGAAGTAAG
* * * ** *
43756931 AGCAACGTCATCTCCTCGAAATTGAAGTAGAATGGATAACACATCTTCATCTCTGAAATTGAAGT
66 AGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTTATCTCTGAAATTGAAGT
* *
43756996 AAGAGCAACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGA
131 AAGAGCAACGCCATCTCCTCGAAATTGAAGTAAAGTGGATAACACATCTTTATCTCTGAAATTGA
43757061 AGTAAGAGC
196 AGTAAGAGC
*
43757070 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAAG
1 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTCATCTCTGAAATTGAAGTAAG
43757135 AGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTTATCTCTGAAATTGAAGT
66 AGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTTATCTCTGAAATTGAAGT
* * * **
43757200 GAGAGCAACGCCATC-CTCTTGAAGTTGAAGTAAAGTGGATAACATGTCTTTATCTCTGAAATTG
131 AAGAGCAACGCCATCTC-CTCGAAATTGAAGTAAAGTGGATAACACATCTTTATCTCTGAAATTG
43757264 AAGTAAGAGC
195 AAGTAAGAGC
* *
43757274 AACGTCATC-CTCTTGAAATTGAAGTAGAGTGGAT-A-ACA---TGA---CT----TTGAAGTAA
1 AACGTCATCTC-CTCGAAATTGAAGTAGAGTGGATAACACATCTTCATCTCTGAAATTGAAGTAA
* *
43757326 GAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTGGATAACATGACTTT
65 GAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTT
43757375 GAAGTAAAAG
Statistics
Matches: 285, Mismatches: 18, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
192 56 0.20
196 2 0.01
199 2 0.01
202 3 0.01
203 3 0.01
204 219 0.77
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (204 bp):
AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTCATCTCTGAAATTGAAGTAAG
AGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTTATCTCTGAAATTGAAGT
AAGAGCAACGCCATCTCCTCGAAATTGAAGTAAAGTGGATAACACATCTTTATCTCTGAAATTGA
AGTAAGAGC
Found at i:43757313 original size:68 final size:68
Alignment explanation
Indices: 43756866--43757311 Score: 725
Period size: 68 Copynumber: 6.6 Consensus size: 68
43756856 TGCAGGTCTT
*
43756866 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTCATCTCTGAAATTGAAGTAAG
1 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAAG
43756931 AGC
66 AGC
* *
43756934 AACGTCATCTCCTCGAAATTGAAGTAGAATGGATAACACATCTTCATCTCTGAAATTGAAGTAAG
1 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAAG
43756999 AGC
66 AGC
43757002 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAAG
1 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAAG
43757067 AGC
66 AGC
43757070 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAAG
1 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAAG
43757135 AGC
66 AGC
* * ** *
43757138 AACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTTATCTCTGAAATTGAAGTGAG
1 AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAAG
43757203 AGC
66 AGC
* * * * **
43757206 AACGCCATC-CTCTTGAAGTTGAAGTAAAGTGGATAACATGTCTTTATCTCTGAAATTGAAGTAA
1 AACGTCATCTC-CTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAA
43757270 GAGC
65 GAGC
*
43757274 AACGTCATC-CTCTTGAAATTGAAGTAGAGTGGATAACA
1 AACGTCATCTC-CTCGAAATTGAAGTAGAGTGGATAACA
43757312 TGACTTTGAA
Statistics
Matches: 362, Mismatches: 15, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
67 1 0.00
68 361 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (68 bp):
AACGTCATCTCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAATTGAAGTAAG
AGC
Found at i:43757347 original size:56 final size:56
Alignment explanation
Indices: 43757261--43757421 Score: 286
Period size: 56 Copynumber: 2.9 Consensus size: 56
43757251 ATCTCTGAAA
43757261 TTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTGGATAACATGACT
1 TTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTGGATAACATGACT
43757317 TTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTGGATAACATGACT
1 TTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTGGATAACATGACT
* * *
43757373 TTGAAGTAAAAGCAACGTCATCCTCTTGAAATTGGAGTAAAGTTGGATA
1 TTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAG-TGGATA
43757422 GCAAGTCTTT
Statistics
Matches: 101, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
56 95 0.94
57 6 0.06
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (56 bp):
TTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTGGATAACATGACT
Found at i:43757377 original size:31 final size:31
Alignment explanation
Indices: 43757286--43757377 Score: 74
Period size: 31 Copynumber: 3.2 Consensus size: 31
43757276 CGTCATCCTC
43757286 TTGAAATTGAAGTAGAGTGGATAACATGACT
1 TTGAAATTGAAGTAGAGTGGATAACATGACT
* ** *
43757317 TTG-AAGT-AAG-AGCA-ACG-T--CAT-CCT
1 TTGAAATTGAAGTAG-AGTGGATAACATGACT
43757341 CTTGAAATTGAAGTAGAGTGGATAACATGACT
1 -TTGAAATTGAAGTAGAGTGGATAACATGACT
43757373 TTGAA
1 TTGAA
43757378 GTAAAAGCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 20
0.61 0.11 0.28
Matches are distributed among these distances:
24 2 0.05
25 6 0.14
26 3 0.07
27 5 0.12
28 6 0.14
29 5 0.12
30 3 0.07
31 11 0.26
32 2 0.05
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (31 bp):
TTGAAATTGAAGTAGAGTGGATAACATGACT
Found at i:43757782 original size:31 final size:29
Alignment explanation
Indices: 43757727--43757797 Score: 97
Period size: 31 Copynumber: 2.4 Consensus size: 29
43757717 AATGTTTGAA
*
43757727 TTAATTTTAAATTCATTTTTAAATTTATC
1 TTAAATTTAAATTCATTTTTAAATTTATC
* *
43757756 TTAAATTTAAATTTACTTATTTAAATTTATT
1 TTAAATTTAAATTCA-TT-TTTAAATTTATC
43757787 TTAAATTTAAA
1 TTAAATTTAAA
43757798 CCTAATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 13 0.35
30 2 0.05
31 22 0.59
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.56
Consensus pattern (29 bp):
TTAAATTTAAATTCATTTTTAAATTTATC
Found at i:43757794 original size:11 final size:11
Alignment explanation
Indices: 43757725--43757795 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
43757715 TTAATGTTTG
*
43757725 AATTAATTTTA
1 AATTTATTTTA
*
43757736 AATTCATTTTTA
1 AATTTA-TTTTA
*
43757748 AATTTATCTTA
1 AATTTATTTTA
*
43757759 AATTTAAATTT-
1 AATTT-ATTTTA
*
43757770 -ACTTA-TTTA
1 AATTTATTTTA
43757779 AATTTATTTTA
1 AATTTATTTTA
43757790 AATTTA
1 AATTTA
43757796 AACCTAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
8 3 0.06
9 1 0.02
10 7 0.15
11 24 0.50
12 13 0.27
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTATTTTA
Found at i:43757907 original size:16 final size:16
Alignment explanation
Indices: 43757868--43757907 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
43757858 GGCCCAAATT
43757868 AAAGGCCCGATTACAA
1 AAAGGCCCGATTACAA
43757884 AAAGGGCCCGATTACAA
1 AAA-GGCCCGATTACAA
*
43757901 GAAGGCC
1 AAAGGCC
43757908 AATTGGGCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.40, C:0.25, G:0.25, T:0.10
Consensus pattern (16 bp):
AAAGGCCCGATTACAA
Found at i:43758820 original size:20 final size:18
Alignment explanation
Indices: 43758792--43758835 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
43758782 AAAACCAAAC
43758792 AAAAAAATAGA-AAGAAATA
1 AAAAAAATA-ATAAG-AATA
43758811 AAAAATAATAATAAGAATA
1 AAAAA-AATAATAAGAATA
43758830 AAAAAA
1 AAAAAA
43758836 GAAGCTTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.04
19 15 0.65
20 7 0.30
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.14
Consensus pattern (18 bp):
AAAAAAATAATAAGAATA
Found at i:43759502 original size:161 final size:162
Alignment explanation
Indices: 43759315--43759659 Score: 421
Period size: 161 Copynumber: 2.1 Consensus size: 162
43759305 AATTTTAATT
* **
43759315 GGTTTATAATTTAGTCCTTTGACTGTTTGACTGTGCCAGAGGCTGCCACGTGTC-ATGTTTTGGA
1 GGTTTATAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCAAT-TTTTGGA
* * * *
43759379 TTATTTATGAATTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCC-CAAATCAACT-TTA
65 TTATTTATGAATTTAGTCCCTTCTATTTTTAATTTATTTTAATTCAATCCTCAAATCAACTGTTA
*
43759442 TTTTAATTACGAAATTAGCCCAATAA-ATTTTCAA
130 -TTTAATTACAAAATTAGCCCAA-AATATTTTCAA
* * * *
43759476 GGTTTATAAACTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGTCACGTGTCAATTTTTGGCT
1 GGTTTATAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCAATTTTTGGAT
* * * * * *
43759541 TATTTCTGCATTTAGTCCCTTCTATTTTTAATTTATTTTTATTCAGTCCTTAAATTAACTGTTAT
66 TATTTATGAATTTAGTCCCTTCTATTTTTAATTTATTTTAATTCAATCCTCAAATCAACTGTTAT
* * *
43759606 TTAATTACAAAATTGGTCCAAAATTTTTTCAA
131 TTAATTACAAAATTAGCCCAAAATATTTTCAA
*
43759638 AGTTT-TCAAATTAGTCCTTTGA
1 GGTTTAT-AAATTAGTCCTTTGA
43759660 AATCTGGATA
Statistics
Matches: 156, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
161 99 0.63
162 54 0.35
163 3 0.02
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (162 bp):
GGTTTATAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCAATTTTTGGAT
TATTTATGAATTTAGTCCCTTCTATTTTTAATTTATTTTAATTCAATCCTCAAATCAACTGTTAT
TTAATTACAAAATTAGCCCAAAATATTTTCAA
Found at i:43759777 original size:30 final size:30
Alignment explanation
Indices: 43759731--43759815 Score: 116
Period size: 30 Copynumber: 2.8 Consensus size: 30
43759721 CCTTAAATTG
* *
43759731 TCCAGAAATCATATTTTGACCCCAAAACTTT
1 TCCA-AAATTATATTTTGACCCCAAAACGTT
*
43759762 TCTAAAATTATATTTTGACCCCAAAACGTT
1 TCCAAAATTATATTTTGACCCCAAAACGTT
* *
43759792 TCCAAAATTACATTTTAACCCCAA
1 TCCAAAATTATATTTTGACCCCAA
43759816 TTTCATCGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 45 0.94
31 3 0.06
ACGTcount: A:0.38, C:0.25, G:0.05, T:0.33
Consensus pattern (30 bp):
TCCAAAATTATATTTTGACCCCAAAACGTT
Found at i:43759869 original size:59 final size:59
Alignment explanation
Indices: 43759795--43760254 Score: 608
Period size: 59 Copynumber: 7.8 Consensus size: 59
43759785 AAACGTTTCC
* * * *
43759795 AAAATTACA-TTTTAACCCCAATTTCATCGAAAATTACAATTTTACCCCCAAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTT
* * * *
43759853 AGAATTCCATTTTTAACCCTGATTTCACCGAAAATTACCATTTTACGCCCGAAA-CTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTAC-CCCCAAATCTTTT
* * *
43759912 AATATTCCATTTTTAACCCTGATTTCACAC-AAAATTACCATTTTACCCCCGAAA-CTTCT
1 AAAATTCCATTTTTAACCCCGATTTCAC-CGAAAATTACCATTTTACCCCC-AAATCTTTT
* *
43759971 -AAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAAGCTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTT
* * *
43760029 AAAATTCTATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCTCGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTT
* * * * * *
43760088 AAAATTCTATTTTTAACCCTGATTTCATCAAAAATTACCATTTTACCCCCGAAGCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTT
*
43760147 AAAATTCCATTTTTAACCCCGATTTCACCGAAATTTACCATTTTACCCCCAAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTT
* ** *
43760206 AAAATTCCATTTTTAACCCCGATTACGTC-AAAATTACCATTTTGCCCCC
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCC
43760255 GGGTATCCAT
Statistics
Matches: 360, Mismatches: 35, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
57 4 0.01
58 78 0.22
59 271 0.75
60 7 0.02
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTT
Found at i:43759983 original size:28 final size:28
Alignment explanation
Indices: 43759884--43759991 Score: 80
Period size: 28 Copynumber: 3.8 Consensus size: 28
43759874 ATTTCACCGA
43759884 AAATTACCATTTT-ACGCCCGAAACTTCT
1 AAATTACCATTTTAAC-CCCGAAACTTCT
* * * *
43759912 AATATT-CCATTTTTAACCCTGATTTCAC-ACA
1 AA-ATTACCA-TTTTAACCCCGA---AACTTCT
*
43759943 AAATTACCATTTTACCCCCGAAACTTCT
1 AAATTACCATTTTAACCCCGAAACTTCT
43759971 AAATT-CCATTTTTAACCCCGA
1 AAATTACCA-TTTTAACCCCGA
43759992 TTTCACCGAA
Statistics
Matches: 61, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
27 5 0.08
28 22 0.36
29 11 0.18
30 15 0.25
31 6 0.10
32 2 0.03
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (28 bp):
AAATTACCATTTTAACCCCGAAACTTCT
Found at i:43760102 original size:176 final size:177
Alignment explanation
Indices: 43759795--43760248 Score: 684
Period size: 176 Copynumber: 2.6 Consensus size: 177
43759785 AAACGTTTCC
* * * * *
43759795 AAAATTACA-TTTTAACCCCAATTTCATCGAAAATTACAATTTTACCCCCAAATCTTTTAGAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTTAAAATT
* *
43759859 CCATTTTTAACCCTGATTTCACCGAAAATTACCATTTTACGCCCGAAACTTCTAATATTCCATTT
66 CCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACGCCCGAAACTTCTAAAATTCCATTT
43759924 TTAACCCTGATTTCA-CACAAAATTACCATTTTACCCCCGAAACTTCT
131 TTAACCCTGATTTCATCA-AAAATTACCATTTTACCCCCGAAACTTCT
* *
43759971 -AAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAAGCTTCTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTTAAAATT
* * * *
43760035 CTATTTTTAACCCCGATTTCACCGAAAATTACCATTTTAC-CCTCGAATCTTTTAAAATTCTATT
66 CCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACGCC-CGAAACTTCTAAAATTCCATT
* *
43760099 TTTAACCCTGATTTCATCAAAAATTACCATTTTACCCCCGAAGCTTTT
130 TTTAACCCTGATTTCATCAAAAATTACCATTTTACCCCCGAAACTTCT
*
43760147 AAAATTCCATTTTTAACCCCGATTTCACCGAAATTTACCATTTTACCCCCAAATCTTTTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTTAAAATT
* **
43760212 CCATTTTTAACCCCGATTACGTC-AAAATTACCATTTT
66 CCATTTTTAACCCCGATTTCACCGAAAATTACCATTTT
43760249 GCCCCCGGGT
Statistics
Matches: 252, Mismatches: 22, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
175 9 0.04
176 161 0.64
177 82 0.33
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (177 bp):
AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCAAATCTTTTAAAATT
CCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACGCCCGAAACTTCTAAAATTCCATTT
TTAACCCTGATTTCATCAAAAATTACCATTTTACCCCCGAAACTTCT
Found at i:43760219 original size:29 final size:29
Alignment explanation
Indices: 43759743--43760254 Score: 111
Period size: 29 Copynumber: 17.4 Consensus size: 29
43759733 CAGAAATCAT
* * *
43759743 ATTTTGACCCCAAAACTTTTCTAAAATTA-T
1 ATTTT-ACCCCCAAA-TCTTCTAAAATTACC
* *
43759773 ATTTTGA-CCCCAAAACGTTTCCAAAATTA-C
1 ATTTT-ACCCCCAAATC--TTCTAAAATTACC
* * * * *
43759803 ATTTTAACCCCAATTTCATCGAAAATTACA
1 ATTTTACCCCCAA-ATCTTCTAAAATTACC
* *
43759833 ATTTTACCCCCAAATCTTTTAGAATT-CC
1 ATTTTACCCCCAAATCTTCTAAAATTACC
** ** ** *
43759861 ATTTTTAACCCTGATTTCACCGAAAATTACC
1 A-TTTT-ACCCCCAAATCTTCTAAAATTACC
* *
43759892 ATTTTACGCCCGAAA-CTTCTAATATT-CC
1 ATTTTAC-CCCCAAATCTTCTAAAATTACC
* ** *
43759920 ATTTTTA-ACCCTGAT-TTCACACAAAATTACC
1 A-TTTTACCCCCAAATCTT--C-TAAAATTACC
43759951 ATTTTACCCCCGAAA-CTTCT-AAATT-CC
1 ATTTTACCCCC-AAATCTTCTAAAATTACC
* ** ** *
43759978 ATTTTTAACCCCGATTTCACCGAAAATTACC
1 A-TTTT-ACCCCCAAATCTTCTAAAATTACC
* *
43760009 ATTTTACCCCCAAAGCTTCTAAAATT-CT
1 ATTTTACCCCCAAATCTTCTAAAATTACC
* ** ** *
43760037 ATTTTTAACCCCGATTTCACCGAAAATTACC
1 A-TTTT-ACCCCCAAATCTTCTAAAATTACC
* * * *
43760068 ATTTTACCCTCGAATCTTTTAAAATT-CT
1 ATTTTACCCCCAAATCTTCTAAAATTACC
** ** * *
43760096 ATTTTTAACCCTGATTTCATCAAAAATTACC
1 A-TTTT-ACCCCCAAATCTTCTAAAATTACC
* * *
43760127 ATTTTACCCCCGAAGCTTTTAAAATT-CC
1 ATTTTACCCCCAAATCTTCTAAAATTACC
* ** ** * *
43760155 ATTTTTAACCCCGATTTCACCGAAATTTACC
1 A-TTTT-ACCCCCAAATCTTCTAAAATTACC
*
43760186 ATTTTACCCCCAAATCTTTTAAAATT-CC
1 ATTTTACCCCCAAATCTTCTAAAATTACC
* * * *
43760214 ATTTTTAACCCCGATTACGTC-AAAATTACC
1 A-TTTTACCCCCAAAT-CTTCTAAAATTACC
*
43760244 ATTTTGCCCCC
1 ATTTTACCCCC
43760255 GGGTATCCAT
Statistics
Matches: 330, Mismatches: 117, Indels: 71
0.64 0.23 0.14
Matches are distributed among these distances:
27 8 0.02
28 25 0.08
29 138 0.42
30 136 0.41
31 20 0.06
32 3 0.01
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (29 bp):
ATTTTACCCCCAAATCTTCTAAAATTACC
Found at i:43763677 original size:30 final size:30
Alignment explanation
Indices: 43763641--43763734 Score: 188
Period size: 30 Copynumber: 3.1 Consensus size: 30
43763631 ATATAAAACA
43763641 TTTGACCTAAAGGCATGTACAGTTTATACC
1 TTTGACCTAAAGGCATGTACAGTTTATACC
43763671 TTTGACCTAAAGGCATGTACAGTTTATACC
1 TTTGACCTAAAGGCATGTACAGTTTATACC
43763701 TTTGACCTAAAGGCATGTACAGTTTATACC
1 TTTGACCTAAAGGCATGTACAGTTTATACC
43763731 TTTG
1 TTTG
43763735 GCTTACCTCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (30 bp):
TTTGACCTAAAGGCATGTACAGTTTATACC
Found at i:43769619 original size:30 final size:31
Alignment explanation
Indices: 43769585--43769647 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
43769575 AATAAATAGA
43769585 TAATAT-CAAATTTATACATGAAGTTTGATT
1 TAATATGCAAATTTATACATGAAGTTTGATT
* ** * *
43769615 TAATATGTATTTTTATATATGAATTTTGATT
1 TAATATGCAAATTTATACATGAAGTTTGATT
43769646 TA
1 TA
43769648 GTGTAATTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 6 0.22
31 21 0.78
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.51
Consensus pattern (31 bp):
TAATATGCAAATTTATACATGAAGTTTGATT
Found at i:43771164 original size:29 final size:29
Alignment explanation
Indices: 43771085--43771301 Score: 139
Period size: 29 Copynumber: 7.4 Consensus size: 29
43771075 TAAAAATCAT
43771085 ATTTTGACCCCTGAACTTTTCC-AAAATT-CC
1 ATTTT-ACCCCTGAA--TTTCCAAAAATTACC
* *
43771115 ATTTTA-ACCTCGATTTCTCCAAAAATTACC
1 ATTTTACCCCT-GAATT-TCCAAAAATTACC
*
43771145 ATTTTACCCCTGAACTTCCAAAAATT-CC
1 ATTTTACCCCTGAATTTCCAAAAATTACC
* *
43771173 ATTTTTAACCCC-GATTTTTCTAAAAATTACC
1 A-TTTT-ACCCCTGA-ATTTCCAAAAATTACC
* * *
43771204 ATTTTACCTCC-GGATGTCTAAAAATT-CC
1 ATTTTACC-CCTGAATTTCCAAAAATTACC
*
43771232 ATTTTTGACCCC-GAATTTTCCCAAAATTACC
1 A-TTTT-ACCCCTGAA-TTTCCAAAAATTACC
* *
43771263 ATTTTA-CCCTTAATTGT-CTAAAATTACC
1 ATTTTACCCCTGAATT-TCCAAAAATTACC
*
43771291 ATTTTGCCCCT
1 ATTTTACCCCT
43771302 CGGTTATCCA
Statistics
Matches: 152, Mismatches: 18, Indels: 35
0.74 0.09 0.17
Matches are distributed among these distances:
27 2 0.01
28 32 0.21
29 55 0.36
30 54 0.36
31 9 0.06
ACGTcount: A:0.29, C:0.27, G:0.06, T:0.38
Consensus pattern (29 bp):
ATTTTACCCCTGAATTTCCAAAAATTACC
Found at i:43771179 original size:59 final size:58
Alignment explanation
Indices: 43771085--43771271 Score: 220
Period size: 59 Copynumber: 3.2 Consensus size: 58
43771075 TAAAAATCAT
*
43771085 ATTTTGACCCCTGAACTTTTCC-AAAATTCCA-TTTTAACCTCGATTTCTCCAAAAATTACC
1 ATTTT-ACCCCTGAAC--TTCCAAAAATTCCATTTTTAACCCCGATTT-TCCAAAAATTACC
*
43771145 ATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCCGATTTTTCTAAAAATTACC
1 ATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCCGA-TTTTCCAAAAATTACC
* * * *
43771204 ATTTTACCTCC-GGA-TGTCTAAAAATTCCATTTTTGACCCCGAATTTTCCCAAAATTACC
1 ATTTTACC-CCTGAACT-TCCAAAAATTCCATTTTTAACCCCG-ATTTTCCAAAAATTACC
43771263 ATTTTACCC
1 ATTTTACCC
43771272 TTAATTGTCT
Statistics
Matches: 114, Mismatches: 7, Indels: 14
0.84 0.05 0.10
Matches are distributed among these distances:
57 4 0.04
58 11 0.10
59 88 0.77
60 11 0.10
ACGTcount: A:0.30, C:0.28, G:0.05, T:0.37
Consensus pattern (58 bp):
ATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCCGATTTTCCAAAAATTACC
Found at i:43771281 original size:59 final size:58
Alignment explanation
Indices: 43771107--43771295 Score: 215
Period size: 59 Copynumber: 3.2 Consensus size: 58
43771097 GAACTTTTCC
* *
43771107 AAAATTCCA-TTTTAACCTCG-ATTTCTCCAAAAATTACCATTTTACCCCTGAACT-TCCA
1 AAAATTCCATTTTTAACCCCGAATTT-TCCAAAAATTACCATTTTA-CCCTGAA-TGTCTA
* * * *
43771165 AAAATTCCATTTTTAACCCCGATTTTTCTAAAAATTACCATTTTACCTCCGGATGTCTA
1 AAAATTCCATTTTTAACCCCGAATTTTCCAAAAATTACCATTTTACC-CTGAATGTCTA
* * *
43771224 AAAATTCCATTTTTGACCCCGAATTTTCCCAAAATTACCATTTTACCCTTAATTGTCT-
1 AAAATTCCATTTTTAACCCCGAATTTTCCAAAAATTACCATTTTACCCTGAA-TGTCTA
43771282 AAAATTACCATTTT
1 AAAATT-CCATTTT
43771296 GCCCCTCGGT
Statistics
Matches: 112, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
58 20 0.18
59 89 0.79
60 3 0.03
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (58 bp):
AAAATTCCATTTTTAACCCCGAATTTTCCAAAAATTACCATTTTACCCTGAATGTCTA
Found at i:43773413 original size:3 final size:3
Alignment explanation
Indices: 43773368--43773397 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
43773358 TGCTGATCAT
43773368 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
43773398 TCAGAGGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:43774053 original size:17 final size:16
Alignment explanation
Indices: 43774031--43774082 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
43774021 ACAAATTAAA
43774031 AATAATTATAAAAGAAT
1 AATAATTATAAAA-AAT
43774048 AATAATTATATTAAAAAT
1 AATAATTATA--AAAAAT
43774066 AA-ATATTATAAAAAAT
1 AATA-ATTATAAAAAAT
43774082 A
1 A
43774083 TTGAATATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 7 0.22
17 11 0.34
18 11 0.34
19 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
AATAATTATAAAAAAT
Found at i:43774151 original size:19 final size:20
Alignment explanation
Indices: 43774129--43774170 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
43774119 AAATAATTTT
43774129 AATAAAATAAAATTAAA-AA
1 AATAAAATAAAATTAAATAA
* * *
43774148 AATATATTATAATTAAATAA
1 AATAAAATAAAATTAAATAA
43774168 AAT
1 AAT
43774171 TAATTTTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AATAAAATAAAATTAAATAA
Found at i:43774165 original size:29 final size:28
Alignment explanation
Indices: 43774119--43774173 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
43774109 AATAGTTTAT
*
43774119 AAATAATTTTAATAAAATAAAATTAAAA
1 AAATAATTATAATAAAATAAAATTAAAA
*
43774147 AAATATATTATAATTAAATAAAATTAA
1 AAATA-ATTATAATAAAATAAAATTAA
43774174 TTTTTGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (28 bp):
AAATAATTATAATAAAATAAAATTAAAA
Found at i:43775056 original size:92 final size:92
Alignment explanation
Indices: 43774933--43776082 Score: 1937
Period size: 92 Copynumber: 12.5 Consensus size: 92
43774923 CAGATCAAAA
* *
43774933 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAGGAGCAAGATGAAGCTTCAAACGTCATTTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
43774998 ATCCTCTTGAAGTTATAGTAAAGTTGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
* * *
43775025 ATAATGAACCTTTATCTCTCTGAAGTTATAGTAGGAGCAAGATGAAGCTTCAAACGTCATTTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
*
43775090 ATCCTCTTG--GTTATAGTAAGGTTGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
43775115 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
* *
43775180 ATCCTCTTGAAGTTATAGAAAAGTCGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
* * * * *
43775207 ATAATGAACCTTTATCTTTCTGAAGTTATAGTAAGAGCAAGATGAAGTTTCAAACATCATTTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
*
43775272 ATCCTCTTGAAGTTATAGTAAAGTGGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
* * * * *
43775299 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAGGAGCAAGATAAAACTTCAAACATCATTTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
43775364 ATCCTCTTGAAGTTATAGTAAAGTTGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
* *
43775391 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAGGAGCAAGATGAAGCTTCAAACGTCATTTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
43775456 ATCCTCTTGAAGTTATAGTAAAGTTGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
*
43775483 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGATTCAAAACGTCAATTCT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTC-AAACGTCAATTCT
43775548 TATCCTCTTGAAGTTATAGTAAAGTTGG
65 TATCCTCTTGAAGTTATAGTAAAGTTGG
*
43775576 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCATTTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
43775641 ATCCTCTTGAAGTTATAGTAAAGTTGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
* *
43775668 ATAACAAACCTTTATCTCTCTGAAGTTATAGCAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
43775733 ATCCTCTTGAAGTTATAGTAAA-TTGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
43775759 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
* *
43775824 ATCCTCTTAAAATTATAGTAAAGTTGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
* *
43775851 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGACGAAGCTTCAAGCGTCAATTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
* *
43775916 ATCCTTTTGAAGTTATAGTAAAGTGGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
* * *
43775943 ACAACGAACCTTTATCTTTCTGAAGTTATAGTAAGAGAAAGATGAAGCTTCAAACGTCAATTCTT
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
43776008 ATCCTCTTGAAGTTATAGTAAAGTTGG
66 ATCCTCTTGAAGTTATAGTAAAGTTGG
* * *
43776035 ATAACGAACCTTTATCTCTCTGAAGTTGTAGTAAGAGTAAGATAAAGC
1 ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGC
43776083 CTCGACATCA
Statistics
Matches: 999, Mismatches: 55, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
90 86 0.09
91 87 0.09
92 736 0.74
93 90 0.09
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (92 bp):
ATAACGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTT
ATCCTCTTGAAGTTATAGTAAAGTTGG
Found at i:43775325 original size:40 final size:40
Alignment explanation
Indices: 43775270--43775516 Score: 122
Period size: 40 Copynumber: 5.6 Consensus size: 40
43775260 ACATCATTTC
43775270 TTATCCTCTTGAAGTTATAGTAAAGTGGGATAACGAACCT
1 TTATCCTCTTGAAGTTATAGTAAAGTGGGATAACGAACCT
* *** *
43775310 TTAT-CTCTCTGAAGTTATAGTAGGAGCAAGATAAAACTTCAAACATCATTT
1 TTATCCTCT-TGAAGTTATAGTA-AAGTGGGAT--AA---CGAAC--C---T
*
43775361 CTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCT
1 -TTATCCTCTTGAAGTTATAGTAAAGTGGGATAACGAACCT
** * **
43775402 TTAT-CTCTCTGAAGTTATAGTAGGAGCAAGATGAAGCTTCAAACGTCATTT
1 TTATCCTCT-TGAAGTTATAGT---A--AAG-TG--GGAT--AACG-AACCT
*
43775453 CTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACCT
1 -TTATCCTCTTGAAGTTATAGTAAAGTGGGATAACGAACCT
43775494 TTAT-CTCTCTGAAGTTATAGTAA
1 TTATCCTCT-TGAAGTTATAGTAA
43775517 GAGCAAGATG
Statistics
Matches: 156, Mismatches: 22, Indels: 58
0.66 0.09 0.25
Matches are distributed among these distances:
39 12 0.08
40 51 0.33
41 8 0.05
42 4 0.03
43 3 0.02
44 3 0.02
45 3 0.02
46 10 0.06
47 3 0.02
48 3 0.02
49 3 0.02
50 4 0.03
51 8 0.05
52 33 0.21
53 8 0.05
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (40 bp):
TTATCCTCTTGAAGTTATAGTAAAGTGGGATAACGAACCT
Found at i:43776874 original size:19 final size:20
Alignment explanation
Indices: 43776852--43776890 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
43776842 CTTTGAAAAC
43776852 CAAACAGAA-GCATTC-AATA
1 CAAACA-AAGGCATTCGAATA
43776871 CAAACAAAGGCATTCGAATA
1 CAAACAAAGGCATTCGAATA
43776891 GCCACACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 12 0.67
20 4 0.22
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.15
Consensus pattern (20 bp):
CAAACAAAGGCATTCGAATA
Found at i:43777199 original size:9 final size:9
Alignment explanation
Indices: 43777185--43777237 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
43777175 TATTAACAAA
43777185 AATAATATT
1 AATAATATT
*
43777194 AATAATAAT
1 AATAATATT
43777203 AATAA-A-T
1 AATAATATT
43777210 -ATAATATT
1 AATAATATT
*
43777218 AAT-ATTTT
1 AATAATATT
43777226 AAATAATATT
1 -AATAATATT
43777236 AA
1 AA
43777238 ATAAAAAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
6 4 0.11
7 2 0.06
8 6 0.17
9 20 0.56
10 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATAATATT
Found at i:43777230 original size:24 final size:25
Alignment explanation
Indices: 43777165--43777231 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 25
43777155 AAAAGCAATA
*
43777165 ATTAATATTTTATTAACAAAAATAAT
1 ATTAATATTTTA-TAATAAAAATAAT
* * *
43777191 ATTAATA-ATAATAATAAATATAAT
1 ATTAATATTTTATAATAAAAATAAT
43777215 ATTAATATTTTA-AATAA
1 ATTAATATTTTATAATAA
43777232 TATTAAATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
24 23 0.68
25 4 0.12
26 7 0.21
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTAATATTTTATAATAAAAATAAT
Found at i:43778272 original size:30 final size:29
Alignment explanation
Indices: 43778238--43778422 Score: 162
Period size: 30 Copynumber: 6.2 Consensus size: 29
43778228 CAAAAATGGC
*
43778238 ATTTTGACCCCTAAACTTTTCCAAAATTAT
1 ATTTT-ACCCCTAAACTTTTCTAAAATTAT
** * *
43778268 ATTTTAATCTTAAAACTTTT-TAAAAATTAC
1 ATTTTACCCCT-AAACTTTTCT-AAAATTAT
*
43778298 ATTTTATCCCCCAAACTTATT-TAAAATTAT
1 ATTTTA-CCCCTAAACTT-TTCTAAAATTAT
* *
43778328 ATTTTAACCTTAAAACTTTT-TGAAAATTAT
1 ATTTTACCCCT-AAACTTTTCT-AAAATTAT
43778358 ATTTTAACCCCTAAACTTTTCTAAAATTAT
1 ATTTT-ACCCCTAAACTTTTCTAAAATTAT
* *
43778388 ATTTTAACCCCAAAAC-TTTCTATAAATTAC
1 ATTTT-ACCCCTAAACTTTTCTA-AAATTAT
43778418 ATTTT
1 ATTTT
43778423 TGCCCTCGAT
Statistics
Matches: 129, Mismatches: 17, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
29 14 0.11
30 106 0.82
31 9 0.07
ACGTcount: A:0.38, C:0.17, G:0.01, T:0.44
Consensus pattern (29 bp):
ATTTTACCCCTAAACTTTTCTAAAATTAT
Found at i:43778301 original size:60 final size:59
Alignment explanation
Indices: 43778237--43778422 Score: 248
Period size: 60 Copynumber: 3.1 Consensus size: 59
43778227 CCAAAAATGG
* *
43778237 CATTTTGACCCCTAAACTTTTCCAAAATTATATTTTAATCTTAAAACTTTTTAAAAATTA
1 CATTTT-ACCCCTAAACTTTTCTAAAATTATATTTTAACCTTAAAACTTTTTAAAAATTA
* *
43778297 CATTTTATCCCCCAAACTTATT-TAAAATTATATTTTAACCTTAAAACTTTTTGAAAATTA
1 CATTTTA-CCCCTAAACTT-TTCTAAAATTATATTTTAACCTTAAAACTTTTTAAAAATTA
* ** * *
43778357 TATTTTAACCCCTAAACTTTTCTAAAATTATATTTTAACCCCAAAACTTTCTATAAATTA
1 CATTTT-ACCCCTAAACTTTTCTAAAATTATATTTTAACCTTAAAACTTTTTAAAAATTA
43778417 CATTTT
1 CATTTT
43778423 TGCCCTCGAT
Statistics
Matches: 110, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
59 3 0.03
60 104 0.95
61 3 0.03
ACGTcount: A:0.38, C:0.18, G:0.01, T:0.44
Consensus pattern (59 bp):
CATTTTACCCCTAAACTTTTCTAAAATTATATTTTAACCTTAAAACTTTTTAAAAATTA
Found at i:43778332 original size:90 final size:90
Alignment explanation
Indices: 43778237--43778422 Score: 209
Period size: 90 Copynumber: 2.1 Consensus size: 90
43778227 CCAAAAATGG
* * *
43778237 CATTTTGACCCCT-AAACTTTTCCAAAATTATATTTTAA-TCTTAAAACTTTT-TAAAAATTACA
1 CATTTT-AACCCTAAAACTTTTCCAAAATTATATTTTAACCCCT-AAACTTTTCT-AAAATTACA
* * *
43778299 TTTTATCCCCCAAACTTATTTA-AAATTA
63 TTTTAACCCCAAAACTT-TCTATAAATTA
* * ** *
43778327 TATTTTAACCTTAAAACTTTTTGAAAATTATATTTTAACCCCTAAACTTTTCTAAAATTATATTT
1 CATTTTAACCCTAAAACTTTTCCAAAATTATATTTTAACCCCTAAACTTTTCTAAAATTACATTT
43778392 TAACCCCAAAACTTTCTATAAATTA
66 TAACCCCAAAACTTTCTATAAATTA
43778417 CATTTT
1 CATTTT
43778423 TGCCCTCGAT
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
89 7 0.09
90 70 0.88
91 3 0.04
ACGTcount: A:0.38, C:0.18, G:0.01, T:0.44
Consensus pattern (90 bp):
CATTTTAACCCTAAAACTTTTCCAAAATTATATTTTAACCCCTAAACTTTTCTAAAATTACATTT
TAACCCCAAAACTTTCTATAAATTA
Found at i:43778539 original size:58 final size:58
Alignment explanation
Indices: 43778401--43778683 Score: 281
Period size: 57 Copynumber: 4.9 Consensus size: 58
43778391 TTAACCCCAA
* * *
43778401 AACTTTCTATAAATTACATTTTTGCCCTCGATTTTAACCAAAATTA-CATTTTGGCCC-CC
1 AACTTTCTA-AAATTCCATTTTTGCCCTCGATTTT-ACCAAAATTACCATTTT-ACCCTCG
* *
43778460 AAGTTT-TACAAAATTCTATTTTTGCCCTCGATTTTACCAAAATTACCATTTTACCCTCG
1 AACTTTCT--AAAATTCCATTTTTGCCCTCGATTTTACCAAAATTACCATTTTACCCTCG
* * * * *
43778519 AACTTTCTAAAATTTCATTTTTACCCTCGATTTCACCAAAA-TACCATTTTACCCCCA
1 AACTTTCTAAAATTCCATTTTTGCCCTCGATTTTACCAAAATTACCATTTTACCCTCG
* ** ** *
43778576 AATTTTCTAAAATTCCA-TTTTAACCTTAATTTTACCAAAATTACCATTTTACCCTTG
1 AACTTTCTAAAATTCCATTTTTGCCCTCGATTTTACCAAAATTACCATTTTACCCTCG
* * * * *
43778633 AACTTTCCAAAATCCCATTTTTG-ACTCAATTTTGACCGAAATTACCATTTT
1 AACTTTCTAAAATTCCATTTTTGCCCTCGATTTT-ACCAAAATTACCATTTT
43778684 GCCTCCCGAG
Statistics
Matches: 188, Mismatches: 28, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
56 19 0.10
57 64 0.34
58 63 0.34
59 40 0.21
60 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.40
Consensus pattern (58 bp):
AACTTTCTAAAATTCCATTTTTGCCCTCGATTTTACCAAAATTACCATTTTACCCTCG
Found at i:43778587 original size:28 final size:27
Alignment explanation
Indices: 43778490--43778653 Score: 94
Period size: 28 Copynumber: 5.7 Consensus size: 27
43778480 TTTGCCCTCG
*
43778490 ATTTTACCAAAATTACCATTTTACCCTCGA
1 ATTTT-CCAAAA-TACCATTTTACCC-CCA
* * ** * *
43778520 ACTTTCTAAAATTTCATTTTTACCCTCG
1 ATTTTCCAAAATACCA-TTTTACCCCCA
*
43778548 ATTTCACCAAAATACCATTTTACCCCCAA
1 ATTT-TCCAAAATACCATTTTACCCCC-A
* * * **
43778577 ATTTTCTAAAATTCCATTTTAACCTTA
1 ATTTTCCAAAATACCATTTTACCCCCA
**
43778604 ATTTTACCAAAATTACCATTTTACCCTTGA
1 ATTTT-CCAAAA-TACCATTTTACCC-CCA
* *
43778634 ACTTTCCAAAATCCCATTTT
1 ATTTTCCAAAATACCATTTT
43778654 TGACTCAATT
Statistics
Matches: 102, Mismatches: 26, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
27 6 0.06
28 44 0.43
29 42 0.41
30 10 0.10
ACGTcount: A:0.32, C:0.26, G:0.02, T:0.40
Consensus pattern (27 bp):
ATTTTCCAAAATACCATTTTACCCCCA
Found at i:43778595 original size:57 final size:58
Alignment explanation
Indices: 43778380--43778683 Score: 280
Period size: 58 Copynumber: 5.2 Consensus size: 58
43778370 AAACTTTTCT
* * * *
43778380 AAAATTA-TATTTTAACCCCAAAACTTTCTATAAATTACATTTTTGCCCTCGATTTTAACC
1 AAAATTACCATTTT-ACCCCCAAACTTTCTA-AAATTCCATTTTTACCCTCGATTTT-ACC
* ** * *
43778440 AAAATTA-CATTTTGGCCCCCAAGTTTTAC-AAAATTCTATTTTTGCCCTCGATTTTACC
1 AAAATTACCATTTT-ACCCCCAAACTTT-CTAAAATTCCATTTTTACCCTCGATTTTACC
* * * *
43778498 AAAATTACCATTTTACCCTCGAACTTTCTAAAATTTCATTTTTACCCTCGATTTCACC
1 AAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTACCCTCGATTTTACC
* * **
43778556 AAAA-TACCATTTTACCCCCAAATTTTCTAAAATTCCA-TTTTAACCTTAATTTTACC
1 AAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTACCCTCGATTTTACC
*** * * *
43778612 AAAATTACCATTTTACCCTTGAACTTTCCAAAATCCCATTTTTGA--CTCAATTTTGACC
1 AAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTT-ACCCTCGATTTT-ACC
*
43778670 GAAATTACCATTTT
1 AAAATTACCATTTT
43778684 GCCTCCCGAG
Statistics
Matches: 204, Mismatches: 33, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
56 19 0.09
57 65 0.32
58 67 0.33
59 30 0.15
60 22 0.11
61 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.39
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTACCCTCGATTTTACC
Found at i:43778631 original size:29 final size:29
Alignment explanation
Indices: 43778411--43778683 Score: 172
Period size: 29 Copynumber: 9.4 Consensus size: 29
43778401 AACTTTCTAT
* *
43778411 AAATTA-CATTTTTGCCCTCGATTTTAACCA
1 AAATTACCA-TTTTACCCTCAATTTT-ACCA
* *
43778441 AAATTA-CATTTTGGCCCCCAAGTTTTA-CA
1 AAATTACCATTTT-ACCCTCAA-TTTTACCA
* * *
43778470 AAATT-CTATTTTTGCCCTCGATTTTACCA
1 AAATTACCA-TTTTACCCTCAATTTTACCA
* *
43778499 AAATTACCATTTTACCCTCGAACTTT-CTA
1 AAATTACCATTTTACCCTC-AATTTTACCA
* * *
43778528 AAATT-TCATTTTTACCCTCGATTTCACCA
1 AAATTACCA-TTTTACCCTCAATTTTACCA
* *
43778557 AAA-TACCATTTTACCCCCAAATTTT-CTA
1 AAATTACCATTTTACCCTC-AATTTTACCA
* *
43778585 AAATT-CCATTTTAACCTTAATTTTACCA
1 AAATTACCATTTTACCCTCAATTTTACCA
* *
43778613 AAATTACCATTTTACCCTTGAACTTT-CCA
1 AAATTACCATTTTACCC-TCAATTTTACCA
* *** *
43778642 AAA-TCCCATTTTTGACTCAATTTTGACCG
1 AAATTACCATTTTACCCTCAATTTT-ACCA
43778671 AAATTACCATTTT
1 AAATTACCATTTT
43778684 GCCTCCCGAG
Statistics
Matches: 190, Mismatches: 35, Indels: 36
0.73 0.13 0.14
Matches are distributed among these distances:
27 12 0.06
28 51 0.27
29 84 0.44
30 39 0.21
31 4 0.02
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.40
Consensus pattern (29 bp):
AAATTACCATTTTACCCTCAATTTTACCA
Found at i:43779659 original size:3 final size:3
Alignment explanation
Indices: 43779651--43779678 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
43779641 GAGAACATTT
43779651 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
43779679 AGAAACCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:43782138 original size:21 final size:22
Alignment explanation
Indices: 43782072--43782138 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 22
43782062 TTGAATAAAA
**
43782072 TTTTACTGTTTCGATTGCTATT
1 TTTTACTGTTTTAATTGCTATT
* *
43782094 TTTTGCTGTTTTAGTAT--TATT
1 TTTTACTGTTTTAAT-TGCTATT
43782115 TTTTACTGTTTTAATTGCTATT
1 TTTTACTGTTTTAATTGCTATT
43782137 TT
1 TT
43782139 GATGTTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
20 1 0.03
21 17 0.47
22 17 0.47
23 1 0.03
ACGTcount: A:0.15, C:0.09, G:0.12, T:0.64
Consensus pattern (22 bp):
TTTTACTGTTTTAATTGCTATT
Found at i:43782147 original size:21 final size:21
Alignment explanation
Indices: 43782123--43782165 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
43782113 TTTTTTACTG
*
43782123 TTTTAATTGCTATTTTGATGT
1 TTTTAATTACTATTTTGATGT
**
43782144 TTTTTTTTACTATTTTGATGT
1 TTTTAATTACTATTTTGATGT
43782165 T
1 T
43782166 GTTTTTGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.05, G:0.12, T:0.67
Consensus pattern (21 bp):
TTTTAATTACTATTTTGATGT
Found at i:43782168 original size:24 final size:24
Alignment explanation
Indices: 43782135--43782208 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
43782125 TTAATTGCTA
**
43782135 TTTTGATGTT-TTTTT-TTACTA-
1 TTTTGATGTTGTTTTTGTTGTTAT
43782156 TTTTGATGTTGTTTTTGTTGTTAT
1 TTTTGATGTTGTTTTTGTTGTTAT
* * *
43782180 TTTTGTTGTTGTTTTTGCTGCTAT
1 TTTTGATGTTGTTTTTGTTGTTAT
43782204 TTTTG
1 TTTTG
43782209 TTGTCATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
21 10 0.22
22 5 0.11
23 4 0.09
24 26 0.58
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.70
Consensus pattern (24 bp):
TTTTGATGTTGTTTTTGTTGTTAT
Found at i:43782170 original size:21 final size:21
Alignment explanation
Indices: 43782132--43782171 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
43782122 GTTTTAATTG
*
43782132 CTATTTTGATGTTTTTTTTTA
1 CTATTTTGATGTTGTTTTTTA
43782153 CTATTTTGATGTTGTTTTT
1 CTATTTTGATGTTGTTTTT
43782172 GTTGTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.05, G:0.12, T:0.70
Consensus pattern (21 bp):
CTATTTTGATGTTGTTTTTTA
Found at i:43782171 original size:12 final size:12
Alignment explanation
Indices: 43782156--43782249 Score: 71
Period size: 12 Copynumber: 7.8 Consensus size: 12
43782146 TTTTTTACTA
*
43782156 TTTTGATGTTGT
1 TTTTGTTGTTGT
*
43782168 TTTTGTTGTTAT
1 TTTTGTTGTTGT
43782180 TTTTGTTGTTGT
1 TTTTGTTGTTGT
* * *
43782192 TTTTGCTGCTAT
1 TTTTGTTGTTGT
**
43782204 TTTTGTTGTCAT
1 TTTTGTTGTTGT
* *
43782216 TTTTGCTGCTGT
1 TTTTGTTGTTGT
* * *
43782228 TTTAGTTATTAT
1 TTTTGTTGTTGT
*
43782240 TTTGGTTGTT
1 TTTTGTTGTT
43782250 TGGATGTTAT
Statistics
Matches: 62, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 62 1.00
ACGTcount: A:0.07, C:0.05, G:0.20, T:0.67
Consensus pattern (12 bp):
TTTTGTTGTTGT
Found at i:43782196 original size:36 final size:36
Alignment explanation
Indices: 43782156--43782230 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
43782146 TTTTTTACTA
* * * * *
43782156 TTTTGATGTTGTTTTTGTTGTTATTTTTGTTGTTGT
1 TTTTGATGCTATTTTTGTTGTCATTTTTGCTGCTGT
*
43782192 TTTTGCTGCTATTTTTGTTGTCATTTTTGCTGCTGT
1 TTTTGATGCTATTTTTGTTGTCATTTTTGCTGCTGT
43782228 TTT
1 TTT
43782231 AGTTATTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.05, C:0.07, G:0.20, T:0.68
Consensus pattern (36 bp):
TTTTGATGCTATTTTTGTTGTCATTTTTGCTGCTGT
Found at i:43782209 original size:24 final size:24
Alignment explanation
Indices: 43782156--43782230 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
43782146 TTTTTTACTA
* * *
43782156 TTTTGATGTTGTTTTTGTTGTTAT
1 TTTTGTTGTTGTTTTTGCTGCTAT
43782180 TTTTGTTGTTGTTTTTGCTGCTAT
1 TTTTGTTGTTGTTTTTGCTGCTAT
** *
43782204 TTTTGTTGTCATTTTTGCTGCTGT
1 TTTTGTTGTTGTTTTTGCTGCTAT
43782228 TTT
1 TTT
43782231 AGTTATTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.05, C:0.07, G:0.20, T:0.68
Consensus pattern (24 bp):
TTTTGTTGTTGTTTTTGCTGCTAT
Found at i:43782241 original size:36 final size:36
Alignment explanation
Indices: 43782167--43782248 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 36
43782157 TTTGATGTTG
* * * * *
43782167 TTTTTGTTGTTATTTTTGTTGTTGTTTTTGCTGCTA
1 TTTTTGTTGTCATTTTTGCTGCTGTTTTAGCTACTA
* *
43782203 TTTTTGTTGTCATTTTTGCTGCTGTTTTAGTTATTA
1 TTTTTGTTGTCATTTTTGCTGCTGTTTTAGCTACTA
*
43782239 TTTTGGTTGT
1 TTTTTGTTGT
43782249 TTGGATGTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.07, C:0.06, G:0.20, T:0.67
Consensus pattern (36 bp):
TTTTTGTTGTCATTTTTGCTGCTGTTTTAGCTACTA
Found at i:43794039 original size:19 final size:19
Alignment explanation
Indices: 43794015--43794055 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
43794005 TTTTATAGAG
*
43794015 ATTCTAATTAGGAGAGATT
1 ATTCTAATTAAGAGAGATT
*
43794034 ATTCTAATTAAGAGATATT
1 ATTCTAATTAAGAGAGATT
43794053 ATT
1 ATT
43794056 TCCTTAGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (19 bp):
ATTCTAATTAAGAGAGATT
Found at i:43796424 original size:13 final size:13
Alignment explanation
Indices: 43796406--43796433 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
43796396 GAACCGAGTA
43796406 TAACTTTAATGAT
1 TAACTTTAATGAT
43796419 TAACTTTAATGAT
1 TAACTTTAATGAT
43796432 TA
1 TA
43796434 TTTGGAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (13 bp):
TAACTTTAATGAT
Found at i:43798858 original size:19 final size:19
Alignment explanation
Indices: 43798834--43798874 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
43798824 TTTTTTAGAG
* *
43798834 ATTCTAATTAGGAGATATT
1 ATTCTAATTAAGAGATACT
43798853 ATTCTAATTAAGAGATACT
1 ATTCTAATTAAGAGATACT
43798872 ATT
1 ATT
43798875 TCCTTAGTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (19 bp):
ATTCTAATTAAGAGATACT
Found at i:43800500 original size:3 final size:3
Alignment explanation
Indices: 43800494--43800521 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
43800484 GATGATGATG
43800494 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
43800522 AGGCAACCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:43814162 original size:23 final size:23
Alignment explanation
Indices: 43814131--43814174 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
43814121 CATTTCATCA
*
43814131 ATACCCAAATGGAAAAATAATAT
1 ATACACAAATGGAAAAATAATAT
43814154 ATACACAAATGGAAAAATAAT
1 ATACACAAATGGAAAAATAAT
43814175 TCGTAATGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.59, C:0.11, G:0.09, T:0.20
Consensus pattern (23 bp):
ATACACAAATGGAAAAATAATAT
Found at i:43814902 original size:4 final size:4
Alignment explanation
Indices: 43814893--43814924 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
43814883 TATGAGCTTC
43814893 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
43814925 TTACTCATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:43816047 original size:57 final size:57
Alignment explanation
Indices: 43815959--43816076 Score: 218
Period size: 57 Copynumber: 2.1 Consensus size: 57
43815949 AAATTGAGTT
* *
43815959 CTTTTTTGATAATTGTCTTAGCTATAAAGTTATAAAGTTGAAATGACAAAGTACTTA
1 CTTTTTAGATAATTGTCATAGCTATAAAGTTATAAAGTTGAAATGACAAAGTACTTA
43816016 CTTTTTAGATAATTGTCATAGCTATAAAGTTATAAAGTTGAAATGACAAAGTACTTA
1 CTTTTTAGATAATTGTCATAGCTATAAAGTTATAAAGTTGAAATGACAAAGTACTTA
43816073 CTTT
1 CTTT
43816077 GGAATGGAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (57 bp):
CTTTTTAGATAATTGTCATAGCTATAAAGTTATAAAGTTGAAATGACAAAGTACTTA
Found at i:43817441 original size:13 final size:15
Alignment explanation
Indices: 43817423--43817454 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
43817413 AAAATATAAT
43817423 AAAATATTA-AAAA-
1 AAAATATTACAAAAG
43817436 AAAATATTACAAAAG
1 AAAATATTACAAAAG
43817451 AAAA
1 AAAA
43817455 CACAAAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 4 0.24
15 4 0.24
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (15 bp):
AAAATATTACAAAAG
Found at i:43820157 original size:37 final size:38
Alignment explanation
Indices: 43820107--43820199 Score: 100
Period size: 37 Copynumber: 2.4 Consensus size: 38
43820097 CGGATAGATT
*
43820107 CGATGAGGTACTGGGTACCACTTTA-CTTCG-ACTAGGC
1 CGATGAGGCACTGGGTACCACTTTATCTTCGAACTA-GC
* ** *
43820144 CGATGAGACACTGGGTGTCACTTTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTACCACTTTA-T-CTTCGAACTAGC
43820184 CGATGAGGCACTGGGT
1 CGATGAGGCACTGGGT
43820200 GCCATTCTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
37 21 0.46
40 21 0.46
41 4 0.09
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.28
Consensus pattern (38 bp):
CGATGAGGCACTGGGTACCACTTTATCTTCGAACTAGC
Found at i:43823922 original size:14 final size:17
Alignment explanation
Indices: 43823890--43823922 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
43823880 AAAAATCCAG
43823890 AAAAATTCTGTGTGAAA
1 AAAAATTCTGTGTGAAA
43823907 AAAAATT-TGT-TGAAA
1 AAAAATTCTGTGTGAAA
43823922 A
1 A
43823923 CACAACAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.52, C:0.03, G:0.15, T:0.30
Consensus pattern (17 bp):
AAAAATTCTGTGTGAAA
Found at i:43836480 original size:26 final size:25
Alignment explanation
Indices: 43836432--43836496 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 25
43836422 GACCCTTGGC
*
43836432 CTTTCACTTACT-AAAAATTCTTGAT
1 CTTTCAC-TACTAAAAAACTCTTGAT
43836457 CTTTCATCTACTAAAAAACTCTTGAT
1 CTTTCA-CTACTAAAAAACTCTTGAT
43836483 CTTTCACCTACTAA
1 CTTTCA-CTACTAA
43836497 CTACTAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
25 10 0.28
26 26 0.72
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.40
Consensus pattern (25 bp):
CTTTCACTACTAAAAAACTCTTGAT
Found at i:43842896 original size:16 final size:17
Alignment explanation
Indices: 43842875--43842906 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
43842865 TAATAGAGTG
43842875 GAAAGAAAA-TGGAGAA
1 GAAAGAAAATTGGAGAA
43842891 GAAAGAAAATTGGAGA
1 GAAAGAAAATTGGAGA
43842907 GGTAGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.31, T:0.09
Consensus pattern (17 bp):
GAAAGAAAATTGGAGAA
Found at i:43853260 original size:12 final size:12
Alignment explanation
Indices: 43853245--43853281 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
43853235 ACAATTCATA
43853245 TCACTTTCAATT
1 TCACTTTCAATT
*
43853257 TCACTTTCACTT
1 TCACTTTCAATT
43853269 TCACTTTCAATT
1 TCACTTTCAATT
43853281 T
1 T
43853282 TGATCACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (12 bp):
TCACTTTCAATT
Found at i:43853264 original size:6 final size:6
Alignment explanation
Indices: 43853245--43853277 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
43853235 ACAATTCATA
*
43853245 TCACTT TCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCA
43853278 ATTTTGATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.21, C:0.30, G:0.00, T:0.48
Consensus pattern (6 bp):
TCACTT
Found at i:43853455 original size:22 final size:22
Alignment explanation
Indices: 43853430--43853473 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
43853420 AACATATAAC
43853430 ATTTCACATATACATTGTTCAT
1 ATTTCACATATACATTGTTCAT
43853452 ATTTCACATATACATTGTTCAT
1 ATTTCACATATACATTGTTCAT
43853474 CACATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (22 bp):
ATTTCACATATACATTGTTCAT
Found at i:43853478 original size:18 final size:20
Alignment explanation
Indices: 43853432--43853481 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
43853422 CATATAACAT
43853432 TTCACATATACATTGTTCATA
1 TTCACATATACATTGTTCA-A
43853453 TTTCACATATACATTGTTC-A
1 -TTCACATATACATTGTTCAA
43853473 -TCACATATA
1 TTCACATATA
43853482 TATCATCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.32
20 1 0.04
22 18 0.64
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (20 bp):
TTCACATATACATTGTTCAA
Found at i:43861539 original size:21 final size:22
Alignment explanation
Indices: 43861489--43861542 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
43861479 GTAAATATTT
*
43861489 AAAA-AATT-AAAAATCTTTAA
1 AAAATAATTAAAAAATCTTCAA
43861509 AAAATAATTAAAAAAT-TTCAA
1 AAAATAATTAAAAAATCTTCAA
* *
43861530 ATAATTATTAAAA
1 AAAATAATTAAAA
43861543 TTATTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.14
21 19 0.66
22 6 0.21
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATAATTAAAAAATCTTCAA
Found at i:43864822 original size:42 final size:42
Alignment explanation
Indices: 43864770--43864852 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
43864760 GAAAGCTGAA
* *
43864770 AGTGAAAGTGCAAAGACTTAGATCCAAAGAGAAAACCAAAGC
1 AGTGAAAGTGCAAAGACTCAAATCCAAAGAGAAAACCAAAGC
* *
43864812 AGTGAGAGTGCAGAGACTCAAATCCAAAGAGAAAACCAAAG
1 AGTGAAAGTGCAAAGACTCAAATCCAAAGAGAAAACCAAAG
43864853 TAATGACGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (42 bp):
AGTGAAAGTGCAAAGACTCAAATCCAAAGAGAAAACCAAAGC
Found at i:43865150 original size:17 final size:18
Alignment explanation
Indices: 43865128--43865163 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
43865118 AGGCAGTAAC
43865128 AGATGGAAAG-AAGAAGA
1 AGATGGAAAGAAAGAAGA
43865145 AGATGGAAAGAAAGAAGA
1 AGATGGAAAGAAAGAAGA
43865163 A
1 A
43865164 AATAAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.33, T:0.06
Consensus pattern (18 bp):
AGATGGAAAGAAAGAAGA
Found at i:43866197 original size:23 final size:23
Alignment explanation
Indices: 43866171--43866228 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
43866161 AAATTGAATC
43866171 AAATCAAAATTTTGTATGGTACA
1 AAATCAAAATTTTGTATGGTACA
43866194 AAATCAAAATTTTGTATGGTACA
1 AAATCAAAATTTTGTATGGTACA
43866217 AAATCAAAATTT
1 AAATCAAAATTT
43866229 ATATATAACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.34
Consensus pattern (23 bp):
AAATCAAAATTTTGTATGGTACA
Found at i:43868119 original size:27 final size:27
Alignment explanation
Indices: 43868081--43868149 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
43868071 ATATTTGGAG
* *
43868081 ATATTTTTTTATTAAT-TAATTAGTTAA
1 ATATTATTTTATTAATAT-ATTACTTAA
*
43868108 ATATTATTTTATTAATATTTTACTTAA
1 ATATTATTTTATTAATATATTACTTAA
43868135 ATATTTATTATTATT
1 ATA-TTATT-TTATT
43868150 TTATTTAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 25 0.69
28 6 0.17
29 5 0.14
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (27 bp):
ATATTATTTTATTAATATATTACTTAA
Found at i:43868139 original size:13 final size:11
Alignment explanation
Indices: 43868112--43868154 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
43868102 AGTTAAATAT
43868112 TATTTTATTAA
1 TATTTTATTAA
43868123 TATTTTACTTAA
1 TATTTTA-TTAA
*
43868135 -ATATTTATTAT
1 TAT-TTTATTAA
43868146 TATTTTATT
1 TATTTTATT
43868155 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:43871458 original size:21 final size:21
Alignment explanation
Indices: 43871423--43871463 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
43871413 CCTTTTCTAA
**
43871423 AGTTAAAAGTTAAAACCATTG
1 AGTTAAAAGACAAAACCATTG
*
43871444 AGTTAAAAGACAAAATCATT
1 AGTTAAAAGACAAAACCATT
43871464 ATATTGTTTA
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:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (21 bp):
AGTTAAAAGACAAAACCATTG
Found at i:43875649 original size:11 final size:12
Alignment explanation
Indices: 43875631--43875664 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
43875621 ACAAAATTCA
43875631 ATTTTATTTATT
1 ATTTTATTTATT
43875643 A-TTTATTT-TT
1 ATTTTATTTATT
43875653 ATTTTATTTATT
1 ATTTTATTTATT
43875665 TATCATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.15
11 14 0.70
12 3 0.15
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTTATTTATT
Found at i:43875661 original size:15 final size:16
Alignment explanation
Indices: 43875641--43875675 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
43875631 ATTTTATTTA
*
43875641 TTATTTATTT-TTATT
1 TTATTTATTTATCATT
43875656 TTATTTATTTATCATT
1 TTATTTATTTATCATT
43875672 TTAT
1 TTAT
43875676 AAATGTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTTATTTATCATT
Found at i:43875672 original size:22 final size:22
Alignment explanation
Indices: 43875631--43875673 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
43875621 ACAAAATTCA
*
43875631 ATTTTATTTATTATTTATTTTT
1 ATTTTATTTATTATTCATTTTT
43875653 ATTTTATTTATT-TATCATTTT
1 ATTTTATTTATTAT-TCATTTT
43875674 ATAAATGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (22 bp):
ATTTTATTTATTATTCATTTTT
Found at i:43875827 original size:21 final size:20
Alignment explanation
Indices: 43875796--43875858 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
43875786 TTATCTATTT
*
43875796 ATAAATATAAATAAATATAA
1 ATAAAAATAAATAAATATAA
*
43875816 ATGAAAAATAAATAAATAAATA
1 AT-AAAAATAAATAAATATA-A
* *
43875838 ATAAAATTAAACAAATATAA
1 ATAAAAATAAATAAATATAA
43875858 A
1 A
43875859 CCAAATGCAC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 4 0.11
21 29 0.81
22 3 0.08
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (20 bp):
ATAAAAATAAATAAATATAA
Found at i:43875832 original size:15 final size:15
Alignment explanation
Indices: 43875802--43875842 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
43875792 ATTTATAAAT
*
43875802 ATAAATAA-ATATAA
1 ATAAATAATAAATAA
43875816 ATGAAA-AATAAATAA
1 AT-AAATAATAAATAA
43875831 ATAAATAATAAA
1 ATAAATAATAAA
43875843 ATTAAACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
ATAAATAATAAATAA
Found at i:43876885 original size:30 final size:30
Alignment explanation
Indices: 43876824--43877045 Score: 193
Period size: 30 Copynumber: 7.4 Consensus size: 30
43876814 AATTTTTTAG
* * *
43876824 AAATTCAAATCTAA-TCTCGAAACTTTTCAA
1 AAATTCAAATTTAACCCTC-AAACTTTCCAA
** *
43876854 AAATTCAAATTCGACCCTCAAATTTTCCAA
1 AAATTCAAATTTAACCCTCAAACTTTCCAA
* * *
43876884 AAATTCTAATTTAACCCTCTAAC-TTCTAA
1 AAATTCAAATTTAACCCTCAAACTTTCCAA
* * **
43876913 AAATTTAAATTTAACCC-CTTAACTTTTTAA
1 AAATTCAAATTTAACCCTC-AAACTTTCCAA
*
43876943 AAATTCAAATTTATCCCTCTAAACTTTCCAAA
1 AAATTCAAATTTAACCCTC-AAACTTTCC-AA
* * *
43876975 AAATT-GAATTTAACCTTCAAACTTTCTAA
1 AAATTCAAATTTAACCCTCAAACTTTCCAA
* *
43877004 AAATTCCAATTTGATCCCT-AAACTTTCCAA
1 AAATTCAAATTT-AACCCTCAAACTTTCCAA
43877034 AAATTCAAATTT
1 AAATTCAAATTT
43877046 GACCTGGTTT
Statistics
Matches: 156, Mismatches: 29, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
28 1 0.01
29 31 0.20
30 92 0.59
31 25 0.16
32 7 0.04
ACGTcount: A:0.41, C:0.22, G:0.02, T:0.36
Consensus pattern (30 bp):
AAATTCAAATTTAACCCTCAAACTTTCCAA
Found at i:43876908 original size:60 final size:60
Alignment explanation
Indices: 43876844--43877045 Score: 205
Period size: 59 Copynumber: 3.4 Consensus size: 60
43876834 CTAATCTCGA
* ** * * *
43876844 AACTTTTCAAAAATTCAAATTCGACCCTCAAATTTTCCAAAAATTCTAATTTAACCCTCT
1 AACTTTCCAAAAATTCAAATTTAACCCTCAAATTTTCTAAAAATTCAAATTTATCCCTCT
* * * *
43876904 AAC-TTCTAAAAATTTAAATTTAACCCCTTAACTTTT-TAAAAATTCAAATTTATCCCTCT
1 AACTTTCCAAAAATTCAAATTTAA-CCCTCAAATTTTCTAAAAATTCAAATTTATCCCTCT
* * * * *
43876963 AAACTTTCCAAAAAATT-GAATTTAACCTTCAAACTTTCTAAAAATTCCAATTTGATCCCT-A
1 -AACTTTCC-AAAAATTCAAATTTAACCCTCAAATTTTCTAAAAATTCAAATTT-ATCCCTCT
43877024 AACTTTCCAAAAATTCAAATTT
1 AACTTTCCAAAAATTCAAATTT
43877046 GACCTGGTTT
Statistics
Matches: 116, Mismatches: 19, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
59 42 0.36
60 37 0.32
61 24 0.21
62 13 0.11
ACGTcount: A:0.40, C:0.22, G:0.01, T:0.37
Consensus pattern (60 bp):
AACTTTCCAAAAATTCAAATTTAACCCTCAAATTTTCTAAAAATTCAAATTTATCCCTCT
Found at i:43878028 original size:5 final size:5
Alignment explanation
Indices: 43878018--43878047 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
43878008 TTTTTGATTA
43878018 TATTT TATTT TATTT TATTT TCATTT TATT
1 TATTT TATTT TATTT TATTT T-ATTT TATT
43878048 GATAAATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TATTT
Done.