Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold19
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: 2266706
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 17655 characters in sequence are not A, C, G, or T
File 15 of 15
Found at i:2205832 original size:8 final size:8
Alignment explanation
Indices: 2205819--2205859 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
2205809 TGTGTCTTTC
2205819 ACAAAAAA
1 ACAAAAAA
2205827 AC-AAAAA
1 ACAAAAAA
2205834 ACAAAAAA
1 ACAAAAAA
*
2205842 CAAAAAAAA
1 -ACAAAAAA
2205851 ACAAAAAA
1 ACAAAAAA
2205859 A
1 A
2205860 ATAACAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 7 0.24
8 15 0.52
9 7 0.24
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
ACAAAAAA
Found at i:2205846 original size:12 final size:11
Alignment explanation
Indices: 2205821--2205869 Score: 62
Period size: 12 Copynumber: 4.2 Consensus size: 11
2205811 TGTCTTTCAC
2205821 AAAAAAACAAA
1 AAAAAAACAAA
*
2205832 AAACAAAAAACAA
1 AAA-AAAACA-AA
2205845 AAAAAAACAAA
1 AAAAAAACAAA
2205856 AAAAATAACAAA
1 AAAAA-AACAAA
2205868 AA
1 AA
2205870 GGGTCCGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 10 0.30
12 18 0.55
13 5 0.15
ACGTcount: A:0.88, C:0.10, G:0.00, T:0.02
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:2205847 original size:22 final size:22
Alignment explanation
Indices: 2205821--2205869 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 22
2205811 TGTCTTTCAC
*
2205821 AAAAAAACAAAAAACAAAAAACAA
1 AAAAAAAC-AAAAA-AAATAACAA
2205845 AAAAAAACAAAAAAAATAACAA
1 AAAAAAACAAAAAAAATAACAA
2205867 AAA
1 AAA
2205870 GGGTCCGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 11 0.46
23 5 0.21
24 8 0.33
ACGTcount: A:0.88, C:0.10, G:0.00, T:0.02
Consensus pattern (22 bp):
AAAAAAACAAAAAAAATAACAA
Found at i:2205849 original size:10 final size:10
Alignment explanation
Indices: 2205819--2205860 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
2205809 TGTGTCTTTC
2205819 ACAAAAAAACA
1 ACAAAAAAA-A
*
2205830 AAAAACAAAAA
1 ACAAA-AAAAA
2205841 ACAAAAAAAA
1 ACAAAAAAAA
2205851 ACAAAAAAAA
1 ACAAAAAAAA
2205861 TAACAAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 15 0.54
11 9 0.32
12 4 0.14
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (10 bp):
ACAAAAAAAA
Found at i:2205868 original size:8 final size:7
Alignment explanation
Indices: 2205822--2205869 Score: 62
Period size: 7 Copynumber: 6.7 Consensus size: 7
2205812 GTCTTTCACA
2205822 AAAAAAC
1 AAAAAAC
2205829 AAAAAAC
1 AAAAAAC
2205836 AAAAAAC
1 AAAAAAC
2205843 AAAAAA-
1 AAAAAAC
*
2205849 AAACAAAA
1 AAA-AAAC
2205857 AAAATAAC
1 AAAA-AAC
2205865 AAAAA
1 AAAAA
2205870 GGGTCCGGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
6 3 0.08
7 25 0.68
8 9 0.24
ACGTcount: A:0.88, C:0.10, G:0.00, T:0.02
Consensus pattern (7 bp):
AAAAAAC
Found at i:2205868 original size:10 final size:10
Alignment explanation
Indices: 2205829--2205869 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
2205819 ACAAAAAAAC
2205829 AAAA-AACAA
1 AAAACAACAA
*
2205838 AAAACAAAAA
1 AAAACAACAA
2205848 AAAACAA-AA
1 AAAACAACAA
*
2205857 AAAATAACAA
1 AAAACAACAA
2205867 AAA
1 AAA
2205870 GGGTCCGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 12 0.43
10 16 0.57
ACGTcount: A:0.88, C:0.10, G:0.00, T:0.02
Consensus pattern (10 bp):
AAAACAACAA
Found at i:2205868 original size:17 final size:15
Alignment explanation
Indices: 2205819--2205869 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
2205809 TGTGTCTTTC
*
2205819 ACAAAAAAACAAAAA
1 ACAAAAAAAAAAAAA
*
2205834 ACAAAAAACAAAAAA
1 ACAAAAAAAAAAAAA
* *
2205849 A-AACAAAAAAAATA
1 ACAAAAAAAAAAAAA
2205863 ACAAAAA
1 ACAAAAA
2205870 GGGTCCGGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.86, C:0.12, G:0.00, T:0.02
Consensus pattern (15 bp):
ACAAAAAAAAAAAAA
Found at i:2207496 original size:61 final size:61
Alignment explanation
Indices: 2207388--2207531 Score: 191
Period size: 61 Copynumber: 2.3 Consensus size: 61
2207378 CTCCATTGCA
* *** *
2207388 CTTTCCAAAAGCCCACACCTCCGTGGCACCCTTTTAAGTCCACAACTCC-GTGATACCTTTTT
1 CTTTCCAAAAGCCCACAACT-CGCAACACCCTTTTAAGTCCACAACTCCAG-GACACCTTTTT
* * *
2207450 CTTTCCAAAAGCCCACAACTCGCAACACTCTTTTAAGTCCATAACTCCAGGGCACCTTTTT
1 CTTTCCAAAAGCCCACAACTCGCAACACCCTTTTAAGTCCACAACTCCAGGACACCTTTTT
2207511 CTTTCCAAAAGCCCACAACTC
1 CTTTCCAAAAGCCCACAACTC
2207532 TGTGGTGCCT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
61 53 0.73
62 20 0.27
ACGTcount: A:0.26, C:0.37, G:0.10, T:0.27
Consensus pattern (61 bp):
CTTTCCAAAAGCCCACAACTCGCAACACCCTTTTAAGTCCACAACTCCAGGACACCTTTTT
Found at i:2207544 original size:61 final size:60
Alignment explanation
Indices: 2207388--2207572 Score: 185
Period size: 61 Copynumber: 3.0 Consensus size: 60
2207378 CTCCATTGCA
* * **
2207388 CTTTCCAAAAGCCCACACCTCCGTGGCACCCTTTTAAGTCCACAACTCC-GTGATACCTTTTT
1 CTTTCCAAAAGCCCACAACT-CGTGG-AACCTTTTAAGTCCACAACTCCAG-GGCACCTTTTT
** *
2207450 CTTTCCAAAAGCCCACAACTCG-CAACACTCTTTTAAGTCCATAACTCCAGGGCACCTTTTT
1 CTTTCCAAAAGCCCACAACTCGTGGA-AC-CTTTTAAGTCCACAACTCCAGGGCACCTTTTT
** * * *
2207511 CTTTCCAAAAGCCCACAACTCTGTGGTGCCTTTTTAAGTCCACGACTCCATGGCACCCTTTT
1 CTTTCCAAAAGCCCACAACTC-GTGGAACC-TTTTAAGTCCACAACTCCAGGGCACCTTTTT
2207573 AAGTCCATGA
Statistics
Matches: 102, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
59 1 0.01
60 1 0.01
61 51 0.50
62 49 0.48
ACGTcount: A:0.24, C:0.35, G:0.12, T:0.29
Consensus pattern (60 bp):
CTTTCCAAAAGCCCACAACTCGTGGAACCTTTTAAGTCCACAACTCCAGGGCACCTTTTT
Found at i:2207572 original size:27 final size:27
Alignment explanation
Indices: 2207542--2207638 Score: 149
Period size: 27 Copynumber: 3.6 Consensus size: 27
2207532 TGTGGTGCCT
2207542 TTTTAAGTCCACGACTCCATGGCACCC
1 TTTTAAGTCCACGACTCCATGGCACCC
*
2207569 TTTTAAGTCCATGACTCCATGGCACCC
1 TTTTAAGTCCACGACTCCATGGCACCC
* * *
2207596 TTTTAAGTCTACGACTCCGTGGCAACC
1 TTTTAAGTCCACGACTCCATGGCACCC
*
2207623 TTTTAAGTCCATGACT
1 TTTTAAGTCCACGACT
2207639 TGGTGGCAAC
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (27 bp):
TTTTAAGTCCACGACTCCATGGCACCC
Found at i:2207818 original size:52 final size:53
Alignment explanation
Indices: 2207679--2207882 Score: 191
Period size: 52 Copynumber: 3.9 Consensus size: 53
2207669 GTTGGTGACA
* * *
2207679 TCTA-CTTCTAAGCCCAATGTCGTTGGCCTTGAATTAACACATTGGCACCTTTT
1 TCTATCTT-TAAGCCCAATGTCGTTGGCCTTGAATCAACACATTGGCACCCTTG
* * * *
2207732 TCTTTCTTCAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCCTTG
1 TCTATCTTTAAGCCCAATGTCGTTGGCCTTGAATCAACACATTGGCACCCTTG
* * * * *
2207785 TC-ATCTTTAAGCCCAATATCGTTGGCCTTGAATCAATATATTGGCA-TCTTC
1 TCTATCTTTAAGCCCAATGTCGTTGGCCTTGAATCAACACATTGGCACCCTTG
** ** * * *
2207836 AATAT-TCTTAAGCCCAACATCGCTAGCCTCGAATCAACACATTGGCA
1 TCTATCT-TTAAGCCCAATGTCGTTGGCCTTGAATCAACACATTGGCA
2207883 TTTTTCTCAT
Statistics
Matches: 124, Mismatches: 24, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
51 4 0.03
52 73 0.59
53 44 0.35
54 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (53 bp):
TCTATCTTTAAGCCCAATGTCGTTGGCCTTGAATCAACACATTGGCACCCTTG
Found at i:2208023 original size:104 final size:104
Alignment explanation
Indices: 2207687--2208027 Score: 299
Period size: 104 Copynumber: 3.3 Consensus size: 104
2207677 CATCTACTTC
* * * * * *
2207687 TAAGCCCAATGTCGTTGGCCTTGAATTAACACATTGGCACCTTTTTCTTTCTTCAAGTCCAATGT
1 TAAGCTCAATATCATTGGCCTTGAATCAACACATTGGCATCTTCTTCTTTC-TCAAGTCCAATGT
* * * *
2207752 CGTTGGCCTTGAATCAGCACATTGGCACCCTTGTCATCTT
65 CGCTAGCCTCGAATCAGCACATTGGCACCTTTGTCATCTT
* * * * * * * * **
2207792 TAAGCCCAATATCGTTGGCCTTGAATCAATATATTGGCATCTTCAAT-ATTCTTAAGCCCAACAT
1 TAAGCTCAATATCATTGGCCTTGAATCAACACATTGGCATCTTC-TTCTTTCTCAAGTCCAATGT
* ** * *
2207856 CGCTAGCCTCGAATCAACACATTGGCATTTTTCTCATTTT
65 CGCTAGCCTCGAATCAGCACATTGGCACCTTTGTCATCTT
* * *** * * *
2207896 TAAG-TCCGATGTCATTCATCTTGAATTAGCACATTGGCATCTTCTTCTTTCTCAAGTCTAATGT
1 TAAGCT-CAATATCATTGGCCTTGAATCAACACATTGGCATCTTCTTCTTTCTCAAGTCCAATGT
* * *
2207960 CACTAGCATCGAATCAGCACATTAGCACCTTTGTCATCTT
65 CGCTAGCCTCGAATCAGCACATTGGCACCTTTGTCATCTT
* *
2208000 TAAGCTCAATATTACTGGCCTTGAATCA
1 TAAGCTCAATATCATTGGCCTTGAATCA
2208028 GCATATTGAC
Statistics
Matches: 177, Mismatches: 55, Indels: 9
0.73 0.23 0.04
Matches are distributed among these distances:
103 1 0.01
104 133 0.75
105 42 0.24
106 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.35
Consensus pattern (104 bp):
TAAGCTCAATATCATTGGCCTTGAATCAACACATTGGCATCTTCTTCTTTCTCAAGTCCAATGTC
GCTAGCCTCGAATCAGCACATTGGCACCTTTGTCATCTT
Found at i:2208058 original size:61 final size:62
Alignment explanation
Indices: 2207993--2208124 Score: 162
Period size: 61 Copynumber: 2.1 Consensus size: 62
2207983 AGCACCTTTG
* * *
2207993 TCATCTTTAAGCTCAATATTACT-GGCCTTGAATCAGCAT-ATTGACACCCTTATCATTCTTC-
1 TCATCTTCAAGCTCAATATTA-TGGGCCCTGAATCAGCATAATTGACACCCTTATCAGTC-TCA
* * * *
2208054 TCATCTTCAAGCTTAATATTATGGGCCCTGAATTAGCATAATTGGCACCTTTATCAGTCTCA
1 TCATCTTCAAGCTCAATATTATGGGCCCTGAATCAGCATAATTGACACCCTTATCAGTCTCA
2208116 TCATCTTCA
1 TCATCTTCA
2208125 TCATCTATAA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
60 1 0.02
61 35 0.57
62 25 0.41
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (62 bp):
TCATCTTCAAGCTCAATATTATGGGCCCTGAATCAGCATAATTGACACCCTTATCAGTCTCA
Found at i:2213555 original size:13 final size:13
Alignment explanation
Indices: 2213523--2213556 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2213513 TGTCACCATG
*
2213523 TATCGAAACAATA
1 TATCGATACAATA
*
2213536 TATCGATACACTA
1 TATCGATACAATA
2213549 TATCGATA
1 TATCGATA
2213557 ATGAGTGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:2213628 original size:19 final size:20
Alignment explanation
Indices: 2213585--2213656 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
2213575 TGGTAGTTTT
*** *
2213585 ATGTATCGATACAATTTAGC
1 ATGTATCGATACAAAGCAAC
* *
2213605 ATGTATCAATACCAAG-AAC
1 ATGTATCGATACAAAGCAAC
*
2213624 ATGTATCGATACAAAGCAAT
1 ATGTATCGATACAAAGCAAC
2213644 ATGTATCGATACA
1 ATGTATCGATACA
2213657 TCTAGGTATG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 16 0.37
20 27 0.63
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (20 bp):
ATGTATCGATACAAAGCAAC
Found at i:2213666 original size:20 final size:20
Alignment explanation
Indices: 2213643--2213695 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
2213633 TACAAAGCAA
2213643 TATGTATCGATACATCTAGG
1 TATGTATCGATACATCTAGG
*
2213663 TATGTATCGATACATCTGGG
1 TATGTATCGATACATCTAGG
2213683 TATGTATCGATAC
1 TATGTATCGATAC
2213696 TTTTTAGGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
TATGTATCGATACATCTAGG
Found at i:2214677 original size:18 final size:18
Alignment explanation
Indices: 2214651--2214692 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2214641 AGGTCAAGAA
*
2214651 TCTTATTTT-GTTTCTTAG
1 TCTTTTTTTGGTTTC-TAG
2214669 TCTTTTTTTGGGTTTCTAG
1 TCTTTTTTT-GGTTTCTAG
2214688 TCTTT
1 TCTTT
2214693 GATCTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.07, C:0.12, G:0.14, T:0.67
Consensus pattern (18 bp):
TCTTTTTTTGGTTTCTAG
Found at i:2219493 original size:22 final size:21
Alignment explanation
Indices: 2219458--2219513 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
2219448 CTTTACAATT
2219458 TATTTATTTATTTACATTAATG
1 TATTTATTTATTTACATT-ATG
* * *
2219480 TATTTGTTTGTTTAGATTATG
1 TATTTATTTATTTACATTATG
*
2219501 TAATTATTTATTT
1 TATTTATTTATTT
2219514 GGTTACTTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (21 bp):
TATTTATTTATTTACATTATG
Found at i:2219565 original size:16 final size:15
Alignment explanation
Indices: 2219552--2219585 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 15
2219542 TATTAATTTA
2219552 TTTTATATTTAATTACT
1 TTTTA-ATTTAATTA-T
2219569 TTTTAATTTAATTAT
1 TTTTAATTTAATTAT
2219584 TT
1 TT
2219586 CTTATTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 9 0.53
17 5 0.29
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTAATTTAATTAT
Found at i:2219702 original size:26 final size:24
Alignment explanation
Indices: 2219668--2219717 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
2219658 AAAGTTGATA
2219668 AAATTTCTTAGAAAAATATTATATAT
1 AAATTTCTTA-AAAAATATTA-ATAT
*
2219694 AAATTTCTTAAAAAATTTTAATAT
1 AAATTTCTTAAAAAATATTAATAT
2219718 CTATTAGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.17
25 9 0.39
26 10 0.43
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (24 bp):
AAATTTCTTAAAAAATATTAATAT
Found at i:2227273 original size:13 final size:13
Alignment explanation
Indices: 2227255--2227281 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2227245 ACATTATGCT
2227255 TTGTATCGATACA
1 TTGTATCGATACA
2227268 TTGTATCGATACA
1 TTGTATCGATACA
2227281 T
1 T
2227282 GTTCACTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2227317 original size:20 final size:19
Alignment explanation
Indices: 2227265--2227321 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
2227255 TTGTATCGAT
*
2227265 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGC
* * *
2227284 TCACTGTATTGATACATGC
1 ACATTGTATCGATACATGC
2227303 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
2227322 AAACTAGCAG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:2227375 original size:20 final size:20
Alignment explanation
Indices: 2227350--2227403 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
2227340 TTACCACTGT
2227350 TTGTATCGATACATGA-CACA
1 TTGTATCGATACATGATCA-A
*
2227370 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATCAA
*
2227390 TTGTATCAATACAT
1 TTGTATCGATACAT
2227404 TGCTTCTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGATCAA
Found at i:2229738 original size:11 final size:12
Alignment explanation
Indices: 2229704--2229746 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
2229694 GAAAAGAATT
*
2229704 TTTTATTATTTTA
1 TTTT-TTATTATA
2229717 TTTTGTTATTA-A
1 TTTT-TTATTATA
2229729 TTTTTTATTATA
1 TTTTTTATTATA
2229741 TTTTTT
1 TTTTTT
2229747 TAAATTTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 6 0.22
12 12 0.44
13 9 0.33
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (12 bp):
TTTTTTATTATA
Found at i:2229747 original size:13 final size:13
Alignment explanation
Indices: 2229702--2229748 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
2229692 ATGAAAAGAA
2229702 TTTTTTATTAT-T
1 TTTTTTATTATAT
* *
2229714 TTATTTTGTTATTAA
1 TT-TTTTATTA-TAT
2229729 TTTTTTATTATAT
1 TTTTTTATTATAT
2229742 TTTTTTA
1 TTTTTTA
2229749 AATTTTACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
12 2 0.07
13 16 0.57
14 8 0.29
15 2 0.07
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTTTTATTATAT
Found at i:2230717 original size:31 final size:31
Alignment explanation
Indices: 2230670--2230760 Score: 103
Period size: 31 Copynumber: 2.9 Consensus size: 31
2230660 TTGTTGTGTT
* * *
2230670 CGTGGAAGCTGGAAGAGGGTCGAGCTGCTAC
1 CGTGGAAACTGAAAGAGGCTCGAGCTGCTAC
*
2230701 CGTGGAAACTGAAAGAGGCTCGAGCTGCTAG
1 CGTGGAAACTGAAAGAGGCTCGAGCTGCTAC
* * *
2230732 CGTGGAAGCT-AGAAGAAGCTCGAGTTGCT
1 CGTGGAAACTGA-AAGAGGCTCGAGCTGCT
2230761 GGTTTCGGGT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
30 1 0.02
31 51 0.98
ACGTcount: A:0.26, C:0.19, G:0.37, T:0.18
Consensus pattern (31 bp):
CGTGGAAACTGAAAGAGGCTCGAGCTGCTAC
Found at i:2231350 original size:31 final size:31
Alignment explanation
Indices: 2231303--2231368 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
2231293 TTCTTTCCAT
*
2231303 TTGCTTGTGTCCCCCATGATTGCATGCTACA
1 TTGCATGTGTCCCCCATGATTGCATGCTACA
*
2231334 TTGCATGTGTCTCCCATGATTGCATGCTACA
1 TTGCATGTGTCCCCCATGATTGCATGCTACA
2231365 TTGC
1 TTGC
2231369 CTTGCATGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.36
Consensus pattern (31 bp):
TTGCATGTGTCCCCCATGATTGCATGCTACA
Found at i:2231427 original size:9 final size:9
Alignment explanation
Indices: 2231415--2231468 Score: 54
Period size: 9 Copynumber: 5.7 Consensus size: 9
2231405 GCATTTCATG
2231415 ATTTTTTTT
1 ATTTTTTTT
2231424 ATTTTTTTT
1 ATTTTTTTT
* *
2231433 ATTTCTATTA
1 ATTT-TTTTT
*
2231443 ATTTTTATT
1 ATTTTTTTT
2231452 ATTATTTTTT
1 ATT-TTTTTT
2231462 AATTTTT
1 -ATTTTT
2231469 GATTTCTACT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
9 18 0.50
10 15 0.42
11 3 0.08
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:2231448 original size:19 final size:20
Alignment explanation
Indices: 2231424--2231468 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
2231414 GATTTTTTTT
*
2231424 ATTTTTTTTATT-TCTATTA
1 ATTTTTATTATTATCTATTA
* *
2231443 ATTTTTATTATTATTTTTTA
1 ATTTTTATTATTATCTATTA
2231463 ATTTTT
1 ATTTTT
2231469 GATTTCTACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (20 bp):
ATTTTTATTATTATCTATTA
Found at i:2234908 original size:79 final size:80
Alignment explanation
Indices: 2234730--2235014 Score: 288
Period size: 79 Copynumber: 3.6 Consensus size: 80
2234720 AGAAATGACA
** ** * * * * ** *
2234730 GGGTTGGAGTATTATCGATGGTGGACAATCGATGTTTTGGAAATAAAACTGGGATTGGAGTATCC
1 GGGTTGGAGTATCCTCGATTATGGAAAATCGATATTTTAGAAATAAAGCCAGGATTAGAGTATCC
* *
2234795 CTCTCGCAAATAATG
66 CTCTCGAAAATAACG
* *
2234810 GGGTTGGAGTATCCTCGATTATAGAAAATTGATATTTTTA-AAATAAAGCCAGGATTAGAGTATC
1 GGGTTGGAGTATCCTCGATTATGGAAAATCGATA-TTTTAGAAATAAAGCCAGGATTAGAGTATC
*
2234874 CCT-TCAAAAATAACG
65 CCTCTCGAAAATAACG
* * * * * *
2234889 GGGTTGGAGTATCCCCGATTATGGAAGATCGATGTTTTAGAAATAAAGTCAGGGTTAGAATAT-C
1 GGGTTGGAGTATCCTCGATTATGGAAAATCGATATTTTAGAAATAAAGCCAGGATTAGAGTATCC
* *
2234953 TTCTCGGAAATAACG
66 CTCTCGAAAATAACG
** * *
2234968 GGGTTAAAGTATCCTCGATTGTGGAAAATCAATATTTTAGAAATAAA
1 GGGTTGGAGTATCCTCGATTATGGAAAATCGATATTTTAGAAATAAA
2235015 ATTGGGGTTG
Statistics
Matches: 168, Mismatches: 34, Indels: 7
0.80 0.16 0.03
Matches are distributed among these distances:
78 7 0.04
79 108 0.64
80 49 0.29
81 4 0.02
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (80 bp):
GGGTTGGAGTATCCTCGATTATGGAAAATCGATATTTTAGAAATAAAGCCAGGATTAGAGTATCC
CTCTCGAAAATAACG
Found at i:2235047 original size:51 final size:51
Alignment explanation
Indices: 2234975--2235082 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 51
2234965 ACGGGGTTAA
* ** * *
2234975 AGTATCCTCGATTGTGGAAAATCAAT-ATTTTAGAAATAAAATTGGGGTTGG
1 AGTATCCCCGATTGTAAAAAATCAATGA-TTTAGAAATAAAATCGAGGTTGG
** *
2235026 AGTATCCCCGATTGTAAAAAATTGATGATTTGGAAATAAAATCGAGGTTGG
1 AGTATCCCCGATTGTAAAAAATCAATGATTTAGAAATAAAATCGAGGTTGG
2235077 AGTATC
1 AGTATC
2235083 TCCTCAGAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 47 0.98
52 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.31
Consensus pattern (51 bp):
AGTATCCCCGATTGTAAAAAATCAATGATTTAGAAATAAAATCGAGGTTGG
Found at i:2235122 original size:130 final size:130
Alignment explanation
Indices: 2234888--2235145 Score: 338
Period size: 130 Copynumber: 2.0 Consensus size: 130
2234878 CAAAAATAAC
** * * *
2234888 GGGGTTGGAGTATCCCCGATTATGGAAGATCGATGTTTTAGAAATAAAGTCAGGGTTAGAATATC
1 GGGGTTGGAGTATCCCCGATTATAAAAAATCGATGATTTAGAAATAAAATCAGGGTTAGAATATC
* * * * *
2234953 TTCTCGGAAATAACGGGGTTAAAGTATCCTCGATTGTGGAAAATCAATATTTTAGAAATAAAATT
66 TCCTCAGAAATAACGAGGTTAAAGTATCCCCGATGGTGGAAAATCAATATTTTAGAAATAAAATT
* * * * *
2235018 GGGGTTGGAGTATCCCCGATTGTAAAAAATTGATGATTTGGAAATAAAATC-GAGGTTGGAGTAT
1 GGGGTTGGAGTATCCCCGATTATAAAAAATCGATGATTTAGAAATAAAATCAG-GGTTAGAATAT
** *
2235082 CTCCTCAGAAATAACGAGGTTGGAGTATCCCCGATGGTGGAAAATCGATATTTTAGAAATAAAA
65 CTCCTCAGAAATAACGAGGTTAAAGTATCCCCGATGGTGGAAAATCAATATTTTAGAAATAAAA
2235146 ACATGAATGA
Statistics
Matches: 109, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
129 1 0.01
130 108 0.99
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (130 bp):
GGGGTTGGAGTATCCCCGATTATAAAAAATCGATGATTTAGAAATAAAATCAGGGTTAGAATATC
TCCTCAGAAATAACGAGGTTAAAGTATCCCCGATGGTGGAAAATCAATATTTTAGAAATAAAATT
Found at i:2237521 original size:30 final size:30
Alignment explanation
Indices: 2237480--2237576 Score: 97
Period size: 30 Copynumber: 3.5 Consensus size: 30
2237470 CGATACATTG
2237480 AGAAGTGTATCGATACATCTAGGTAAAACCC
1 AGAA-TGTATCGATACATCTAGGTAAAACCC
*
2237511 AGAATGTATCGATACA---A--T-GAA---
1 AGAATGTATCGATACATCTAGGTAAAACCC
*
2237532 A-AATGTATCGATATATCTAGGTAAAACCC
1 AGAATGTATCGATACATCTAGGTAAAACCC
2237561 AGAATGTATCGATACA
1 AGAATGTATCGATACA
2237577 ATTAAGAATG
Statistics
Matches: 52, Mismatches: 4, Indels: 21
0.68 0.05 0.27
Matches are distributed among these distances:
20 13 0.25
21 1 0.02
23 1 0.02
24 2 0.04
25 2 0.04
26 2 0.04
27 1 0.02
29 1 0.02
30 25 0.48
31 4 0.08
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (30 bp):
AGAATGTATCGATACATCTAGGTAAAACCC
Found at i:2237525 original size:50 final size:49
Alignment explanation
Indices: 2237466--2237596 Score: 199
Period size: 50 Copynumber: 2.6 Consensus size: 49
2237456 ATGCTTGAAA
2237466 GTATCGATACATTGAGAAGTGTATCGATACATCTAGGTAAAACCCAGAAT
1 GTATCGATACATTGAGAA-TGTATCGATACATCTAGGTAAAACCCAGAAT
* * *
2237516 GTATCGATACAATGAAAAATGTATCGATATATCTAGGTAAAACCCAGAAT
1 GTATCGATACATTG-AGAATGTATCGATACATCTAGGTAAAACCCAGAAT
*
2237566 GTATCGATACAATTAAGAATGTATCGATACA
1 GTATCGATAC-ATTGAGAATGTATCGATACA
2237597 AATTGTGGAA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
50 67 0.93
51 5 0.07
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (49 bp):
GTATCGATACATTGAGAATGTATCGATACATCTAGGTAAAACCCAGAAT
Found at i:2243043 original size:2 final size:2
Alignment explanation
Indices: 2243036--2243060 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2243026 TTAAAGACAT
2243036 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 T
2243061 TCTAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2244600 original size:24 final size:24
Alignment explanation
Indices: 2244568--2244621 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
2244558 CCTAGACCAC
2244568 TCCAGTTAGTTTTGTTTTCTTTCA
1 TCCAGTTAGTTTTGTTTTCTTTCA
2244592 TCCAGTTAGTTTTGTTTTCTTTCA
1 TCCAGTTAGTTTTGTTTTCTTTCA
2244616 TCCAGT
1 TCCAGT
2244622 GGGTGGCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.13, C:0.19, G:0.13, T:0.56
Consensus pattern (24 bp):
TCCAGTTAGTTTTGTTTTCTTTCA
Found at i:2244914 original size:353 final size:353
Alignment explanation
Indices: 2244268--2244971 Score: 1408
Period size: 353 Copynumber: 2.0 Consensus size: 353
2244258 TCCTTCAACA
2244268 TGGGTGGCCTTGGTTCGAAACCTAAGCCACTCAATTTTTCACCCACAGCAGTCACAATTTAAAAA
1 TGGGTGGCCTTGGTTCGAAACCTAAGCCACTCAATTTTTCACCCACAGCAGTCACAATTTAAAAA
2244333 CATATTTTTTTGACAATTTTATATCAAAAGGACAAATATAGTGCAGTGGTTGATTCTTTATTGAA
66 CATATTTTTTTGACAATTTTATATCAAAAGGACAAATATAGTGCAGTGGTTGATTCTTTATTGAA
2244398 ATGCATAGATGGCCTAGGTTTGAAACTCAGGCCACTCAATTTTGCAATCATTCATGGAGGTACTA
131 ATGCATAGATGGCCTAGGTTTGAAACTCAGGCCACTCAATTTTGCAATCATTCATGGAGGTACTA
2244463 GTTTAACAGAATTGTTTTGATATTTTAGATCAAAACAATGAATGAGGTCCAGTGGTTAGGTTTTT
196 GTTTAACAGAATTGTTTTGATATTTTAGATCAAAACAATGAATGAGGTCCAGTGGTTAGGTTTTT
2244528 TTCTTTCTTCAGGGTGGCTTGGGTTCAAATCCTAGACCACTCCAGTTAGTTTTGTTTTCTTTCAT
261 TTCTTTCTTCAGGGTGGCTTGGGTTCAAATCCTAGACCACTCCAGTTAGTTTTGTTTTCTTTCAT
2244593 CCAGTTAGTTTTGTTTTCTTTCATCCAG
326 CCAGTTAGTTTTGTTTTCTTTCATCCAG
2244621 TGGGTGGCCTTGGTTCGAAACCTAAGCCACTCAATTTTTCACCCACAGCAGTCACAATTTAAAAA
1 TGGGTGGCCTTGGTTCGAAACCTAAGCCACTCAATTTTTCACCCACAGCAGTCACAATTTAAAAA
2244686 CATATTTTTTTGACAATTTTATATCAAAAGGACAAATATAGTGCAGTGGTTGATTCTTTATTGAA
66 CATATTTTTTTGACAATTTTATATCAAAAGGACAAATATAGTGCAGTGGTTGATTCTTTATTGAA
2244751 ATGCATAGATGGCCTAGGTTTGAAACTCAGGCCACTCAATTTTGCAATCATTCATGGAGGTACTA
131 ATGCATAGATGGCCTAGGTTTGAAACTCAGGCCACTCAATTTTGCAATCATTCATGGAGGTACTA
2244816 GTTTAACAGAATTGTTTTGATATTTTAGATCAAAACAATGAATGAGGTCCAGTGGTTAGGTTTTT
196 GTTTAACAGAATTGTTTTGATATTTTAGATCAAAACAATGAATGAGGTCCAGTGGTTAGGTTTTT
2244881 TTCTTTCTTCAGGGTGGCTTGGGTTCAAATCCTAGACCACTCCAGTTAGTTTTGTTTTCTTTCAT
261 TTCTTTCTTCAGGGTGGCTTGGGTTCAAATCCTAGACCACTCCAGTTAGTTTTGTTTTCTTTCAT
2244946 CCAGTTAGTTTTGTTTTCTTTCATCC
326 CCAGTTAGTTTTGTTTTCTTTCATCC
2244972 TCTTCTTCTT
Statistics
Matches: 351, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
353 351 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (353 bp):
TGGGTGGCCTTGGTTCGAAACCTAAGCCACTCAATTTTTCACCCACAGCAGTCACAATTTAAAAA
CATATTTTTTTGACAATTTTATATCAAAAGGACAAATATAGTGCAGTGGTTGATTCTTTATTGAA
ATGCATAGATGGCCTAGGTTTGAAACTCAGGCCACTCAATTTTGCAATCATTCATGGAGGTACTA
GTTTAACAGAATTGTTTTGATATTTTAGATCAAAACAATGAATGAGGTCCAGTGGTTAGGTTTTT
TTCTTTCTTCAGGGTGGCTTGGGTTCAAATCCTAGACCACTCCAGTTAGTTTTGTTTTCTTTCAT
CCAGTTAGTTTTGTTTTCTTTCATCCAG
Found at i:2244953 original size:24 final size:24
Alignment explanation
Indices: 2244921--2244971 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
2244911 CCTAGACCAC
2244921 TCCAGTTAGTTTTGTTTTCTTTCA
1 TCCAGTTAGTTTTGTTTTCTTTCA
2244945 TCCAGTTAGTTTTGTTTTCTTTCA
1 TCCAGTTAGTTTTGTTTTCTTTCA
2244969 TCC
1 TCC
2244972 TCTTCTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.12, C:0.20, G:0.12, T:0.57
Consensus pattern (24 bp):
TCCAGTTAGTTTTGTTTTCTTTCA
Found at i:2245420 original size:21 final size:20
Alignment explanation
Indices: 2245375--2245427 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
2245365 CTTTTTTTCT
*
2245375 CTTTTTTTTCTTTTTTAACA
1 CTTTTTTTTCTCTTTTAACA
*
2245395 -ATTTTTTTCTCTTTTAACCA
1 CTTTTTTTTCTCTTTTAA-CA
*
2245415 CTTTTTATTCTCT
1 CTTTTTTTTCTCT
2245428 CCCAAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 15 0.56
20 2 0.07
21 10 0.37
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.66
Consensus pattern (20 bp):
CTTTTTTTTCTCTTTTAACA
Found at i:2245574 original size:19 final size:17
Alignment explanation
Indices: 2245553--2245605 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
2245543 TTGTTTTGTT
2245553 TTTTATCTTTTTTTTTAA
1 TTTT-TCTTTTTTTTTAA
*
2245571 TTTTTCTATTTTTTATAA
1 TTTTTCT-TTTTTTTTAA
2245589 CTTTTTCTTTTGTTTTT
1 -TTTTTCTTTT-TTTTT
2245606 GTCATTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 3 0.10
18 16 0.53
19 11 0.37
ACGTcount: A:0.13, C:0.08, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTTCTTTTTTTTTAA
Found at i:2245710 original size:9 final size:9
Alignment explanation
Indices: 2245696--2245737 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
2245686 AAGCCACTTA
2245696 TTTTTTT-T
1 TTTTTTTAT
*
2245704 TTTTTTTGT
1 TTTTTTTAT
2245713 TTTTTTTAT
1 TTTTTTTAT
2245722 TTTTTTTAT
1 TTTTTTTAT
*
2245731 ATTTTTT
1 TTTTTTT
2245738 CAAATAAGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 7 0.23
9 24 0.77
ACGTcount: A:0.07, C:0.00, G:0.02, T:0.90
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:2245925 original size:2 final size:2
Alignment explanation
Indices: 2245918--2245945 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2245908 TAGATTTTGG
2245918 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2245946 TAATGATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2247780 original size:17 final size:16
Alignment explanation
Indices: 2247746--2247784 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2247736 AATGCATATT
**
2247746 AAAATTTTTTTCATTC
1 AAAATTTTTTAAATTC
2247762 AAAATTTTTTAAATGTC
1 AAAATTTTTTAAAT-TC
2247779 AAAATT
1 AAAATT
2247785 GCTCGTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (16 bp):
AAAATTTTTTAAATTC
Found at i:2248123 original size:3 final size:3
Alignment explanation
Indices: 2248115--2248161 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
2248105 TTCCAATGTG
2248115 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2248162 TCCAAAGCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2248319 original size:19 final size:19
Alignment explanation
Indices: 2248280--2248320 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2248270 AAAAATACTT
*
2248280 ATTAAAATATATAGTATAA
1 ATTAAAATATATAGTAAAA
**
2248299 ATTAAAATATATTTTAAAA
1 ATTAAAATATATAGTAAAA
2248318 ATT
1 ATT
2248321 TAAGATCGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
ATTAAAATATATAGTAAAA
Found at i:2248942 original size:13 final size:15
Alignment explanation
Indices: 2248924--2248956 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
2248914 TTTTTAATCA
2248924 TTTTAAATA-T-AAT
1 TTTTAAATATTAAAT
2248937 TTTTAAATATTAAAT
1 TTTTAAATATTAAAT
2248952 TTTTA
1 TTTTA
2248957 TTATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 1 0.06
15 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTAAATATTAAAT
Found at i:2248963 original size:22 final size:22
Alignment explanation
Indices: 2248935--2248993 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
2248925 TTTAAATATA
2248935 ATTTTTAAATATTAAATTT-TT
1 ATTTTTAAATATTAAATTTATT
*
2248956 ATTATTTAAATTATATATATTTATT
1 ATT-TTTAAA-TAT-TAAATTTATT
*
2248981 ATTTTTAATTATT
1 ATTTTTAAATATT
2248994 TATCATTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 3 0.09
22 7 0.22
23 6 0.19
24 11 0.34
25 5 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTTTAAATATTAAATTTATT
Found at i:2249048 original size:2 final size:2
Alignment explanation
Indices: 2249043--2249094 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2249033 TTTTATTTTC
2249043 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2249085 TA TA TA TA TA
1 TA TA TA TA TA
2249095 AAGTAAAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2254029 original size:13 final size:13
Alignment explanation
Indices: 2254011--2254067 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
2254001 CATAAAGTGT
2254011 TGTATCGATACAA
1 TGTATCGATACAA
2254024 TGTATCGATACATAA
1 TGTATCGATAC--AA
2254039 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
2254056 TGTATCGATACA
1 TGTATCGATACA
2254068 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2254046 original size:32 final size:32
Alignment explanation
Indices: 2253991--2254088 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
2253981 TTCAAAGATT
2253991 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
2254024 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
2254056 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
2254088 T
1 T
2254089 TTAAGCTACT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 51 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:2254048 original size:19 final size:18
Alignment explanation
Indices: 2253989--2254086 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
2253979 ATTTCAAAGA
2253989 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
2254008 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
2254024 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
2254040 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
2254056 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
2254072 TTTTGTATCGATACA
1 -TTTGTATCGATACA
2254087 ATTTAAGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
19 24 0.36
20 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:2265233 original size:1 final size:1
Alignment explanation
Indices: 2265223--2265313 Score: 83
Period size: 1 Copynumber: 91.0 Consensus size: 1
2265213 TGGCAATTGG
* * * ** * * * *
2265223 AAAAAGAAAAAAACAAAACAAAAAAAAAGGAAAAAGAAAAAAAAAAACAAAACAAAAAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
2265288 AAAAGAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
2265314 GTGAAGATTT
Statistics
Matches: 70, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:2265272 original size:34 final size:34
Alignment explanation
Indices: 2265224--2265313 Score: 148
Period size: 34 Copynumber: 2.7 Consensus size: 34
2265214 GGCAATTGGA
*
2265224 AAAAGAAAAAAACAAAACAAAAAAAAAGGAAAAAG
1 AAAA-AAAAAAACAAAACAAAAAAAAAGAAAAAAG
2265259 AAAAAAAAAAACAAAACAAAAAAAAAGAAAAAAG
1 AAAAAAAAAAACAAAACAAAAAAAAAGAAAAAAG
2265293 -AAAAAAAAAACAAAA-AAAAAA
1 AAAAAAAAAAACAAAACAAAAAA
2265314 GTGAAGATTT
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
32 6 0.11
33 15 0.28
34 29 0.54
35 4 0.07
ACGTcount: A:0.88, C:0.06, G:0.07, T:0.00
Consensus pattern (34 bp):
AAAAAAAAAAACAAAACAAAAAAAAAGAAAAAAG
Done.