Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013765.1 Kokia drynarioides strain JFW-HI SEQ_128793, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 151254
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 502 characters in sequence are not A, C, G, or T
Found at i:5992 original size:23 final size:25
Alignment explanation
Indices: 5945--5994 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 25
5935 TTCCAATTTG
*
5945 GTATGTACCCTCACAACCTTTTATA
1 GTATGTACCCTCACAACCTTGTATA
5970 GTATGTACCCT-A-AACCTTGTATA
1 GTATGTACCCTCACAACCTTGTATA
5993 GT
1 GT
5995 CTATAGACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 12 0.50
24 1 0.04
25 11 0.46
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (25 bp):
GTATGTACCCTCACAACCTTGTATA
Found at i:9966 original size:28 final size:29
Alignment explanation
Indices: 9914--9969 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
9904 GATTTATTAC
* *
9914 TAATATTTTTAAGTTATAATTAATTATAT
1 TAATAGTTTTAAGTTATAATCAATTATAT
9943 TAATAGTTTTAA-TTATAATCAATTATA
1 TAATAGTTTTAAGTTATAATCAATTATA
9970 ACAAGCATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (29 bp):
TAATAGTTTTAAGTTATAATCAATTATAT
Found at i:16107 original size:20 final size:20
Alignment explanation
Indices: 16082--16137 Score: 82
Period size: 17 Copynumber: 3.0 Consensus size: 20
16072 TGTAATTAAA
16082 TAAACTATTGATGTTATATG
1 TAAACTATTGATGTTATATG
16102 TAAACTATTGA---TATATG
1 TAAACTATTGATGTTATATG
*
16119 CAAACTATTGATGTTATAT
1 TAAACTATTGATGTTATAT
16138 CAATTAGATC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 16 0.50
20 16 0.50
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (20 bp):
TAAACTATTGATGTTATATG
Found at i:16945 original size:22 final size:23
Alignment explanation
Indices: 16887--16946 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
16877 TCATTATTTA
* *
16887 ATAATT-GAATGATCTAATTAAT
1 ATAATTAGAATAATTTAATTAAT
*
16909 ATAA-TATCAATAATTTAA-TAAT
1 ATAATTA-GAATAATTTAATTAAT
16931 ATAATTAGAATAATTT
1 ATAATTAGAATAATTT
16947 GCAGTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
21 1 0.03
22 20 0.65
23 10 0.32
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (23 bp):
ATAATTAGAATAATTTAATTAAT
Found at i:23507 original size:15 final size:18
Alignment explanation
Indices: 23472--23504 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
23462 TGAATAAATT
23472 TAAATATTATATTAAAAA
1 TAAATATTATATTAAAAA
23490 TAAATA-TA-ATTAAAA
1 TAAATATTATATTAAAA
23505 TAAGTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAATATTATATTAAAAA
Found at i:24879 original size:22 final size:22
Alignment explanation
Indices: 24837--24879 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
24827 AATTCAAGTG
*
24837 TCAAATTAAAAAATAATAAATT
1 TCAAATTAAAAAATAAGAAATT
*
24859 TCAAATTATATAAAT-AGAAAT
1 TCAAATTA-AAAAATAAGAAAT
24880 AGAAAATTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (22 bp):
TCAAATTAAAAAATAAGAAATT
Found at i:31795 original size:74 final size:74
Alignment explanation
Indices: 31674--31821 Score: 287
Period size: 74 Copynumber: 2.0 Consensus size: 74
31664 TAAAGCGAGG
31674 ATTAATTTCTGTTAACAATGAATCGATACCAATAAAATTATACTCCTAGTGAAACTCTACAGAGT
1 ATTAATTTCTGTTAACAATGAATCGATACCAATAAAATTATACTCCTAGTGAAACTCTACAGAGT
31739 AACTTTATT
66 AACTTTATT
*
31748 ATTAATTTCTGTTAACAATGAATCGATACCAGTAAAATTATACTCCTAGTGAAACTCTACAGAGT
1 ATTAATTTCTGTTAACAATGAATCGATACCAATAAAATTATACTCCTAGTGAAACTCTACAGAGT
31813 AACTTTATT
66 AACTTTATT
31822 TCAAATTAAA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (74 bp):
ATTAATTTCTGTTAACAATGAATCGATACCAATAAAATTATACTCCTAGTGAAACTCTACAGAGT
AACTTTATT
Found at i:32002 original size:17 final size:17
Alignment explanation
Indices: 31982--32082 Score: 107
Period size: 17 Copynumber: 5.9 Consensus size: 17
31972 GAATCTAATT
31982 TTAAATTTTAAA-TTATC
1 TTAAA-TTTAAATTTATC
* *
31999 TTAAGTTTAAATTTATT
1 TTAAATTTAAATTTATC
*
32016 TTAAATTTAAACTTATC
1 TTAAATTTAAATTTATC
* * *
32033 TTGAGTTTAAATTTATT
1 TTAAATTTAAATTTATC
32050 TTAAATTTAAATTTA-C
1 TTAAATTTAAATTTATC
*
32066 TTTGAATTTAAATTTAT
1 -TTAAATTTAAATTTAT
32083 AATTTAATTA
Statistics
Matches: 68, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
16 6 0.09
17 62 0.91
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (17 bp):
TTAAATTTAAATTTATC
Found at i:32088 original size:7 final size:6
Alignment explanation
Indices: 31999--32089 Score: 57
Period size: 6 Copynumber: 15.7 Consensus size: 6
31989 TTAAATTATC
* * * * *
31999 TTAAGT TTAAAT TT-ATT TTAAAT TTAAAC TT--AT CTTGAGT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT
* * *
32045 TT-ATT TTAAAT TTAAAT TT-ACT TTGAAT TTAAAT TTATAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTA-AAT TTAA
32090 TTAAAAGTTC
Statistics
Matches: 65, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
4 1 0.02
5 14 0.22
6 43 0.66
7 7 0.11
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:32094 original size:34 final size:34
Alignment explanation
Indices: 31979--32082 Score: 142
Period size: 34 Copynumber: 3.1 Consensus size: 34
31969 ATTGAATCTA
31979 ATTTTAAATTTTAAA-TTATCTT-AAGTTTAAATTT
1 ATTTTAAA-TTTAAACTTATCTTGAA-TTTAAATTT
*
32013 ATTTTAAATTTAAACTTATCTTGAGTTTAAATTT
1 ATTTTAAATTTAAACTTATCTTGAATTTAAATTT
*
32047 ATTTTAAATTTAAATTTA-CTTTGAATTTAAATTT
1 ATTTTAAATTTAAACTTATC-TTGAATTTAAATTT
32081 AT
1 AT
32083 AATTTAATTA
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
33 7 0.11
34 56 0.88
35 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (34 bp):
ATTTTAAATTTAAACTTATCTTGAATTTAAATTT
Found at i:32975 original size:29 final size:28
Alignment explanation
Indices: 32938--33242 Score: 156
Period size: 29 Copynumber: 10.6 Consensus size: 28
32928 TCCCCGAACT
*
32938 TTCCAAAAATCACATTTTGACCCCTAAAC
1 TTCCCAAAATCACATTTT-ACCCCTAAAC
** * * *
32967 TTTTCAAAATTATATTTTA-CCCTCGAAC
1 TTCCCAAAATCACATTTTACCCCT-AAAC
* * * *
32995 TTCTCAAAATTATATTTTCACCCCTGAAC
1 TTCCCAAAATCACATTTT-ACCCCTAAAC
* *
33024 TTCTCTAAAATTACATTTT-CCCCTTAAAAC
1 TTC-CCAAAATCACATTTTACCCC-T-AAAC
** *
33054 TTCTAAAAATCACATTTTA-CCCTGAAC
1 TTCCCAAAATCACATTTTACCCCTAAAC
* *
33081 TT-CCAAGAATCACATTTTACCTCGAAAC
1 TTCCCAA-AATCACATTTTACCCCTAAAC
*
33109 TTCCCAAAATTACATTTTTACTCCC-AAAC
1 TTCCCAAAATCACA-TTTTAC-CCCTAAAC
* * * *
33138 TTCCAAAAATCACATTTTTGCCCTTTAAC
1 TTCCCAAAATCACA-TTTTACCCCTAAAC
* * * *
33167 ATCCAAAAATTACCATTTTACCCCTGAAC
1 TTCCCAAAATCA-CATTTTACCCCTAAAC
* * **
33196 AT-CCAAAATTACCATTTTTGCCCTCAAA-
1 TTCCCAAAATCA-CATTTTACCCCT-AAAC
*
33224 TTGCCAAAAATCACATTTT
1 TT-CCCAAAATCACATTTT
33243 TAACCTCAAC
Statistics
Matches: 220, Mismatches: 39, Indels: 34
0.75 0.13 0.12
Matches are distributed among these distances:
26 2 0.01
27 21 0.10
28 61 0.28
29 103 0.47
30 33 0.15
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (28 bp):
TTCCCAAAATCACATTTTACCCCTAAAC
Found at i:33001 original size:28 final size:28
Alignment explanation
Indices: 32964--33213 Score: 158
Period size: 29 Copynumber: 8.8 Consensus size: 28
32954 TTGACCCCTA
* *
32964 AACTTTTCAAAATTATATTTTACCCTCG
1 AACTTCTCAAAATTACATTTTACCCTCG
*
32992 AACTTCTCAAAATTATATTTTCACCC-CTG
1 AACTTCTCAAAATTACATTTT-ACCCTC-G
* **
33021 AACTTCTCTAAAATTACATTTTCCCCTTAA
1 AACTTCTC-AAAATTACATTTTACCC-TCG
* *
33051 AACTTCTAAAAATCACATTTTACCCT-G
1 AACTTCTCAAAATTACATTTTACCCTCG
*
33078 AACTTC-CAAGAATCACATTTTA-CCTCG
1 AACTTCTCAA-AATTACATTTTACCCTCG
* *
33105 AAACTTCCCAAAATTACATTTTTACTCC-CA
1 -AACTTCTCAAAATTACA-TTTTAC-CCTCG
* * **
33135 AACTTC-CAAAAATCACATTTTTGCCCTTT
1 AACTTCTC-AAAATTACA-TTTTACCCTCG
*
33164 AACATC-CAAAAATTACCATTTTACCC-CTG
1 AACTTCTC-AAAATTA-CATTTTACCCTC-G
*
33193 AACATC-CAAAATTACCATTTT
1 AACTTCTCAAAATTA-CATTTT
33214 TGCCCTCAAA
Statistics
Matches: 185, Mismatches: 21, Indels: 32
0.78 0.09 0.13
Matches are distributed among these distances:
26 5 0.03
27 19 0.10
28 51 0.28
29 86 0.46
30 22 0.12
31 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (28 bp):
AACTTCTCAAAATTACATTTTACCCTCG
Found at i:33025 original size:57 final size:56
Alignment explanation
Indices: 32943--33213 Score: 178
Period size: 57 Copynumber: 4.7 Consensus size: 56
32933 GAACTTTCCA
* * *
32943 AAAATCACATTTTGACCCCTAAACTTTTCAAAATTATATTTTACCCTCGAACTTCTC
1 AAAATTACATTTT-ACCCCTGAACTTTTCAAAATTACATTTTACCCTCGAACTTCTC
* * * ** *
33000 AAAATTATATTTTCACCCCTGAACTTCTCTAAAATTACATTTTCCCCTTAAAACTTCTA
1 AAAATTACATTTT-ACCCCTGAACTTTTC-AAAATTACATTTTACCC-TCGAACTTCTC
* * * *
33059 AAAATCACATTTTA-CCCTGAAC-TTCCAAGAATCACATTTTA-CCTCGAAACTTCCC
1 AAAATTACATTTTACCCCTGAACTTTTCAA-AATTACATTTTACCCTCG-AACTTCTC
* * * * ** *
33114 AAAATTACATTTTTACTCCC-AAAC-TTCCAAAAATCACATTTTTGCCCTTTAACATC-C
1 AAAATTACA-TTTTAC-CCCTGAACTTTTC-AAAATTACA-TTTTACCCTCGAACTTCTC
* *
33171 AAAAATTACCATTTTACCCCTGAAC-ATCCAAAATTACCATTTT
1 -AAAATTA-CATTTTACCCCTGAACTTTTCAAAATTA-CATTTT
33214 TGCCCTCAAA
Statistics
Matches: 171, Mismatches: 29, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
54 1 0.01
55 18 0.11
56 17 0.10
57 60 0.35
58 51 0.30
59 24 0.14
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (56 bp):
AAAATTACATTTTACCCCTGAACTTTTCAAAATTACATTTTACCCTCGAACTTCTC
Found at i:33219 original size:28 final size:29
Alignment explanation
Indices: 33139--33219 Score: 103
Period size: 28 Copynumber: 2.8 Consensus size: 29
33129 CTCCCAAACT
* *
33139 TCCAAAAATCA-CATTTTTGCCCTTTAACA
1 TCCAAAAATTACCATTTTTGCCC-TGAACA
**
33168 TCCAAAAATTACCATTTTACCCCTGAACA
1 TCCAAAAATTACCATTTTTGCCCTGAACA
33197 TCC-AAAATTACCATTTTTGCCCT
1 TCCAAAAATTACCATTTTTGCCCT
33220 CAAATTGCCA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 18 0.40
29 18 0.40
30 9 0.20
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTTGCCCTGAACA
Found at i:33244 original size:58 final size:56
Alignment explanation
Indices: 32938--33242 Score: 184
Period size: 58 Copynumber: 5.3 Consensus size: 56
32928 TCCCCGAACT
* * * * *
32938 TTCCAAAAATCACATTTTGACCCCTAAACTTTTCAAAATTA-TA-TTTTACCCTCGAAC
1 TTCCAAAAATCACATTTT-ACCCCTGAAC-TTCCAAAATTACCATTTTTGCCCTC-AAA
* * * *
32995 TTCTC-AAAATTATATTTTCACCCCTGAACTTCTCTAAAATTA-CA-TTTTCCCCTTAAAA
1 TTC-CAAAAATCACATTTT-ACCCCTGAACTTC-C-AAAATTACCATTTTTGCCC-TCAAA
* * *
33053 CTTCTAAAAATCACATTTTA-CCCTGAACTTCCAAGAATCA-CA-TTTT-ACCTCGAAA
1 -TTCCAAAAATCACATTTTACCCCTGAACTTCCAA-AATTACCATTTTTGCCCTC-AAA
* * * * *
33108 CTTCCCAAAATTACATTTTTACTCCC-AAACTTCCAAAAAT-CACATTTTTGCCCTTTAACA
1 -TTCCAAAAATCACA-TTTTAC-CCCTGAACTTCCAAAATTAC-CATTTTTGCCC-TCAA-A
* *
33168 -TCCAAAAATTACCATTTTACCCCTGAACATCCAAAATTACCATTTTTGCCCTCAAA
1 TTCCAAAAATCA-CATTTTACCCCTGAACTTCCAAAATTACCATTTTTGCCCTCAAA
33224 TTGCCAAAAATCACATTTT
1 TT-CCAAAAATCACATTTT
33243 TAACCTCAAC
Statistics
Matches: 197, Mismatches: 29, Indels: 44
0.73 0.11 0.16
Matches are distributed among these distances:
54 1 0.01
55 19 0.10
56 21 0.11
57 59 0.30
58 73 0.37
59 22 0.11
60 2 0.01
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (56 bp):
TTCCAAAAATCACATTTTACCCCTGAACTTCCAAAATTACCATTTTTGCCCTCAAA
Found at i:35041 original size:44 final size:42
Alignment explanation
Indices: 34980--35104 Score: 124
Period size: 44 Copynumber: 2.9 Consensus size: 42
34970 TACTTCGCCT
**
34980 AAAAAAAACAGATTGAGATGAAAACCCGTAAAGGGCGTCTCG
1 AAAAAAAAGGGATTGAGATGAAAACCCGTAAAGGGCGTCTCG
* * * *
35022 AAAAAAAAGAGGGATTGAGATGAAAACCCGCAAAAGGCATCTTG
1 -AAAAAAA-AGGGATTGAGATGAAAACCCGTAAAGGGCGTCTCG
** * *
35066 AAACTAAAGGAATTTTGAGTTGAAAACCCGTAAAGGGCG
1 AAAAAAAAGGGA--TTGAGATGAAAACCCGTAAAGGGCG
35105 ATTCAAATTC
Statistics
Matches: 66, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
42 4 0.06
43 12 0.18
44 50 0.76
ACGTcount: A:0.45, C:0.14, G:0.25, T:0.16
Consensus pattern (42 bp):
AAAAAAAAGGGATTGAGATGAAAACCCGTAAAGGGCGTCTCG
Found at i:36138 original size:198 final size:198
Alignment explanation
Indices: 35773--36733 Score: 1026
Period size: 198 Copynumber: 4.8 Consensus size: 198
35763 TTTGACAAGG
* * * ***
35773 AAGGATTGAGGCCGCAACGGTGAATCCGGTACCTTA-AAAGATGTGAAGGGAAAGGTTGAGGCCG
1 AAGG-TTGAGGCCGCAACGGCGAACCCGGTACC--ACGAAGATACAAAGGGAAAGGTTGAGGCCG
* * * * * * *
35837 CAATGACGAACCCGGTACCTAAGAAGAGGTGATAGGAAAGGTTGAGGTCGCAACGGTGAA-CCAG
63 CAACGGCGAGCCCGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCAG
* * *
35901 TACCATGAAGAGATGAAGGGAAGGATTGAAGTCGCGACGGTGAAT-TCGGTACCTTAAAAGATGT
128 TACCATGAAGAGATGAAGGGAAGGATTGAGGCCGCGACGGTGAATCT-GGTACCTTAAAAGATGC
*
35965 TATGGGA
192 GATGGGA
* * *
35972 ACA-GTTGAGGCCGCAACGGCGAGCCTGGTACCACGAAGATACAAAGGGAAAGGTTGAGGTCGCA
1 A-AGGTTGAGGCCGCAACGGCGAACCCGGTACCACGAAGATACAAAGGGAAAGGTTGAGGCCGCA
* ** * * *
36036 ACAGCGAGCCCAATACCTAAGAAGATGTGATGGGAAAGGTTGAGCCCGCAACGGTGAACCTAGTA
65 ACGGCGAGCCCGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTA
* *
36101 CCATGAAGAGATGAAGGGAAGGATTGAGGCCGCGACGGCGAATCTGGTACCTAAAAAGATGCGAT
130 CCATGAAGAGATGAAGGGAAGGATTGAGGCCGCGACGGTGAATCTGGTACCTTAAAAGATGCGAT
*
36166 AGGA
195 GGGA
* * *
36170 AAGGTTGAGGCCGCATCGACGAACCCGGTACCACGAAGATACAAAGGGAAAAGTTGAGGCCGCAA
1 AAGGTTGAGGCCGCAACGGCGAACCCGGTACCACGAAGATACAAAGGGAAAGGTTGAGGCCGCAA
* * * ** * * *
36235 TGGCGAGCCCGGTACCTAAGAAGATGTAATGGGAAAGGCTGAGGTTGCAACAGCGAACCTAATAC
66 CGGCGAGCCCGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTAC
* * *
36300 CATGAAGAGATAAAGGGAAGGATTGAGGCCGCGACGGTCAATCCGGTACC-TAAGAAGATGCGAT
131 CATGAAGAGATGAAGGGAAGGATTGAGGCCGCGACGGTGAATCTGGTACCTTAA-AAGATGCGAT
36364 GGGA
195 GGGA
* * * *
36368 AAGGTTGAGGCCACAACGGCGAATCCGGTACCACGAAGATACAAAGGGAAAGGTTAAGGCTGCAA
1 AAGGTTGAGGCCGCAACGGCGAACCCGGTACCACGAAGATACAAAGGGAAAGGTTGAGGCCGCAA
* *
36433 CGGCGAGCCTGGTACCTTAA-AAGATGT-AGTGGGAAAAGTTGAGGCCGCAACGGCGAACCCAGT
66 CGGCGAGCCCGGTACC-TAAGAAGATGTGA-TGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGT
* ** ** * * * *
36496 ACCATAAAGATTTGAAGGGAAGGATTGA-GTTGACGACGGAGAATCTAGTACCTTAGAAGATGTG
129 ACCATGAAGAGATGAAGGGAAGGATTGAGGCCG-CGACGGTGAATCTGGTACCTTAAAAGATGCG
*
36560 TTGGGA
193 ATGGGA
* * * * ** * *** *
36566 AAAGATGAGGCTGCAAGGGCGAACCCAATACCATGAAGAT-TTGAGAGG-AAGGATTGAGGCCGG
1 AAGGTTGAGGCCGCAACGGCGAACCCGGTACCACGAAGATACAAAG-GGAAAGG-TTGAGGCCGC
* ** * * * *
36629 GACGGCGAATCCAGTACCTTAGAAGATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCACT
64 AACGGCGAGCCCGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGT
* *
36694 ACCATGAAGACATGAAGGGAAAGG-TTGAGGCCGCAACGGT
129 ACCATGAAGAGATGAAGGG-AAGGATTGAGGCCGCGACGGT
36734 AAACCTAGCA
Statistics
Matches: 635, Mismatches: 111, Indels: 33
0.82 0.14 0.04
Matches are distributed among these distances:
196 1 0.00
197 87 0.14
198 531 0.84
199 15 0.02
200 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.33, T:0.16
Consensus pattern (198 bp):
AAGGTTGAGGCCGCAACGGCGAACCCGGTACCACGAAGATACAAAGGGAAAGGTTGAGGCCGCAA
CGGCGAGCCCGGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTAC
CATGAAGAGATGAAGGGAAGGATTGAGGCCGCGACGGTGAATCTGGTACCTTAAAAGATGCGATG
GGA
Found at i:36751 original size:99 final size:99
Alignment explanation
Indices: 35773--36732 Score: 802
Period size: 99 Copynumber: 9.7 Consensus size: 99
35763 TTTGACAAGG
* * * * * *
35773 AAGGATTGAGGCCGCAACGGTGAATCCGGTACCTTAAAAGATGTGAAGGGAAAGG-TTGAGGCCG
1 AAGG-TTGAGGCCGCAACGGCGAACCCAGTACCAT-GAAGATATGAAGGG-AAGGATTGAGGCCG
* * * * *
35837 CAATGACGAACCCGGTACCTAAGAAGAGGTGATAGGA
63 CAACGGCGAACCTGGTACCTAAGAAGATGTGATGGGA
* * * * * *
35874 AAGGTTGAGGTCGCAACGGTGAA-CCAGTACCATGAAGAGATGAAGGGAAGGATTGAAGTCGCGA
1 AAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGAAGGGAAGGATTGAGGCCGCAA
* * *
35938 CGGTGAA-TTCGGTACCTTAA-AAGATGTTATGGGA
66 CGGCGAACCT-GGTACC-TAAGAAGATGTGATGGGA
* ** * ** *
35972 ACA-GTTGAGGCCGCAACGGCGAGCCTGGTACCACGAAGATACAAAGGGAAAGG-TTGAGGTCGC
1 A-AGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGAAGGG-AAGGATTGAGGCCGC
* * ***
36035 AACAGCGAGCCCAATACCTAAGAAGATGTGATGGGA
64 AACGGCGAACCTGGTACCTAAGAAGATGTGATGGGA
* * * * *
36071 AAGGTTGAGCCCGCAACGGTGAACCTAGTACCATGAAGAGATGAAGGGAAGGATTGAGGCCGCGA
1 AAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGAAGGGAAGGATTGAGGCCGCAA
* * * *
36136 CGGCGAATCTGGTACCTAAAAAGATGCGATAGGA
66 CGGCGAACCTGGTACCTAAGAAGATGTGATGGGA
* * * * ** *
36170 AAGGTTGAGGCCGCATCGACGAACCCGGTACCACGAAGATACAAAGGGAA-AAGTTGAGGCCGCA
1 AAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGAAGGGAAGGA-TTGAGGCCGCA
* * * *
36234 ATGGCGAGCCCGGTACCTAAGAAGATGTAATGGGA
65 ACGGCGAACCTGGTACCTAAGAAGATGTGATGGGA
* ** * * * * * *
36269 AAGGCTGAGGTTGCAACAGCGAACCTAATACCATGAAGAGATAAAGGGAAGGATTGAGGCCGCGA
1 AAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGAAGGGAAGGATTGAGGCCGCAA
*
36334 CGGTC-AATCC-GGTACCTAAGAAGATGCGATGGGA
66 CGG-CGAA-CCTGGTACCTAAGAAGATGTGATGGGA
* * * * ** * *
36368 AAGGTTGAGGCCACAACGGCGAATCCGGTACCACGAAGATACAAAGGGAAAGG-TTAAGGCTGCA
1 AAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGAAGGG-AAGGATTGAGGCCGCA
*
36432 ACGGCGAGCCTGGTACCTTAA-AAGATGT-AGTGGGA
65 ACGGCGAACCTGGTACC-TAAGAAGATGTGA-TGGGA
* * * *
36467 AAAGTTGAGGCCGCAACGGCGAACCCAGTACCATAAAGATTTGAAGGGAAGGATTGAGTTGACG-
1 AAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGAAGGGAAGGATTGAG--GCCGC
* * * * *
36531 -ACGGAGAATCTAGTACCTTAGAAGATGTGTTGGGA
64 AACGGCGAACCTGGTACCTAAGAAGATGTGATGGGA
* * * * * * **
36566 AAAGATGAGGCTGCAAGGGCGAACCCAATACCATGAAGATTTG-AGAGGAAGGATTGAGGCCGGG
1 AAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGAAG-GGAAGGATTGAGGCCGCA
* * *
36630 ACGGCGAATCC-AGTACCTTAGAAGATATGATGGGA
65 ACGGCGAA-CCTGGTACCTAAGAAGATGTGATGGGA
* *
36665 AAGGTTGAGGCCGCAACGGCGAACCCACTACCATGAAGACATGAAGGGAAAGG-TTGAGGCCGCA
1 AAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGAAGGG-AAGGATTGAGGCCGCA
36729 ACGG
65 ACGG
36733 TAAACCTAGC
Statistics
Matches: 682, Mismatches: 147, Indels: 62
0.77 0.16 0.07
Matches are distributed among these distances:
97 7 0.01
98 80 0.12
99 549 0.80
100 40 0.06
101 6 0.01
ACGTcount: A:0.33, C:0.18, G:0.33, T:0.16
Consensus pattern (99 bp):
AAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGATATGAAGGGAAGGATTGAGGCCGCAA
CGGCGAACCTGGTACCTAAGAAGATGTGATGGGA
Found at i:37193 original size:34 final size:34
Alignment explanation
Indices: 37151--37219 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
37141 CCAATTTTAA
*
37151 ATTTTAAATTTAAACTTA-TCTTGAGTTTAAATTT
1 ATTTTAAATTTAAACTTACT-TTGAATTTAAATTT
* *
37185 ATTTTAAATTTCAATTTACTTTGAATTTAAATTT
1 ATTTTAAATTTAAACTTACTTTGAATTTAAATTT
37219 A
1 A
37220 AAATTTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 30 0.97
35 1 0.03
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (34 bp):
ATTTTAAATTTAAACTTACTTTGAATTTAAATTT
Found at i:37200 original size:17 final size:17
Alignment explanation
Indices: 37151--37219 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 17
37141 CCAATTTTAA
*
37151 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* * *
37168 ATCTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
37185 ATTTTAAATTTCAATTT
1 ATTTTAAATTTAAATTT
* *
37202 ACTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
37219 A
1 A
37220 AAATTTAATT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:39026 original size:30 final size:28
Alignment explanation
Indices: 38949--39035 Score: 84
Period size: 30 Copynumber: 3.0 Consensus size: 28
38939 TGCATAAGGT
* *
38949 CCCCGAACTTTCCAAAAATCATGTTTTAA
1 CCCCGAACTTTCC-AAAATTATATTTTAA
** *
38978 CCCCGAAACTTTTTAAAATTATATTTTCAC
1 CCCCG-AACTTTCCAAAATTATATTTT-AA
*
39008 CCCCGAACTTCTCCAAAATTACATTTTA
1 CCCCGAACTT-TCCAAAATTATATTTTA
39036 CCTCTAAAAC
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
29 22 0.47
30 25 0.53
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (28 bp):
CCCCGAACTTTCCAAAATTATATTTTAA
Found at i:39061 original size:29 final size:28
Alignment explanation
Indices: 39013--39206 Score: 169
Period size: 29 Copynumber: 6.8 Consensus size: 28
39003 TTCACCCCCG
* *
39013 AACTTCTCCAAAATTACA-TTTTACCTCTAA
1 AACTT-TCAAAAATCACATTTTTACC-CT-A
*
39043 AACTTTCAAAAATCACATTTTTACCCTC
1 AACTTTCAAAAATCACATTTTTACCCTA
* *
39071 AACTTCCAAGAATCACATTTTTACCCATA
1 AACTTTCAAAAATCACATTTTTACCC-TA
** * *
39100 AACTTTGTAAAATTACATTTTTGCCCCTA
1 AACTTTCAAAAATCACATTTTT-ACCCTA
* * *
39129 AACTTTCTAAAATTACATTTTTACCCCCA
1 AACTTTCAAAAATCACATTTTTA-CCCTA
* *
39158 AAC-TTCCAAAATCACATTTTTGCCCTCA
1 AACTTTCAAAAATCACATTTTTACCCT-A
39186 AA-TTTCCAAAAATCACATTTT
1 AACTTT-CAAAAATCACATTTT
39207 CAACCTCAAA
Statistics
Matches: 137, Mismatches: 20, Indels: 15
0.80 0.12 0.09
Matches are distributed among these distances:
27 3 0.02
28 45 0.33
29 74 0.54
30 15 0.11
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (28 bp):
AACTTTCAAAAATCACATTTTTACCCTA
Found at i:39112 original size:57 final size:56
Alignment explanation
Indices: 39019--39206 Score: 175
Period size: 57 Copynumber: 3.3 Consensus size: 56
39009 CCCGAACTTC
*
39019 TCCAAAATTACA-TTTTACCTCTA-AAACTTTCAAAAATCACATTTTTACCCTCAACT
1 TCCAAAATCACATTTTTACC-C-ACAAACTTTCAAAAATCACATTTTTACCCTCAACT
* ** * * *
39075 TCCAAGAATCACATTTTTACCCATAAACTTTGTAAAATTACATTTTTGCCCCTAAACTT
1 TCCAA-AATCACATTTTTACCCACAAACTTTCAAAAATCACATTTTT-ACCCTCAAC-T
* * * * * *
39134 TCTAAAATTACATTTTTACCCCCAAAC-TTCCAAAATCACATTTTTGCCCTCAAATT
1 TCCAAAATCACATTTTTACCCACAAACTTTCAAAAATCACATTTTTACCCTC-AACT
39190 TCCAAAAATCACATTTT
1 TCC-AAAATCACATTTT
39207 CAACCTCAAA
Statistics
Matches: 107, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
56 13 0.12
57 56 0.52
58 33 0.31
59 5 0.05
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (56 bp):
TCCAAAATCACATTTTTACCCACAAACTTTCAAAAATCACATTTTTACCCTCAACT
Found at i:39198 original size:86 final size:87
Alignment explanation
Indices: 39013--39206 Score: 227
Period size: 86 Copynumber: 2.2 Consensus size: 87
39003 TTCACCCCCG
* * *
39013 AACTTCTCCAAAATTACA-TTTTACCTCTAAAACTTTCAAAAATCACATTTTTACCCTCAACTTC
1 AACTT-TCAAAAATTACATTTTTACCCCTAAAACTTTCAAAAATCACATTTTTACCCCCAACTTC
39077 CAAGAATCACATTTTTACCCATA
65 CAAGAATCACATTTTTACCCATA
** * * *
39100 AACTTTGTAAAATTACATTTTTGCCCCT-AAACTTTCTAAAATTACATTTTTACCCCCAAACTTC
1 AACTTTCAAAAATTACATTTTTACCCCTAAAACTTTCAAAAATCACATTTTTACCCCC-AACTTC
*
39164 CAA-AATCACATTTTTGCCC-TCA
65 CAAGAATCACATTTTTACCCAT-A
*
39186 AA-TTTCCAAAAATCACATTTT
1 AACTTT-CAAAAATTACATTTT
39207 CAACCTCAAA
Statistics
Matches: 92, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
85 4 0.04
86 66 0.72
87 22 0.24
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (87 bp):
AACTTTCAAAAATTACATTTTTACCCCTAAAACTTTCAAAAATCACATTTTTACCCCCAACTTCC
AAGAATCACATTTTTACCCATA
Found at i:39236 original size:30 final size:29
Alignment explanation
Indices: 39137--39226 Score: 92
Period size: 28 Copynumber: 3.1 Consensus size: 29
39127 TAAACTTTCT
* * * * *
39137 AAAATTACATTTTTACCCCCAAACTTCC-
1 AAAATCACATTTTCAACCTCAAATTTCCA
***
39165 AAAATCACATTTTTGCCCTCAAATTTCCA
1 AAAATCACATTTTCAACCTCAAATTTCCA
39194 AAAATCACATTTTCAACCTCAAATTTTCCA
1 AAAATCACATTTTCAACCTCAAA-TTTCCA
39224 AAA
1 AAA
39227 GTTCAATTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
28 24 0.45
29 20 0.38
30 9 0.17
ACGTcount: A:0.39, C:0.28, G:0.01, T:0.32
Consensus pattern (29 bp):
AAAATCACATTTTCAACCTCAAATTTCCA
Found at i:44135 original size:49 final size:51
Alignment explanation
Indices: 44030--44138 Score: 179
Period size: 49 Copynumber: 2.2 Consensus size: 51
44020 TTCTTATTAA
*
44030 AAATGT-TTAACTATTTATTCAAATAAAAAAAATAAAATCTTTCTATTGTT
1 AAATGTATTAACTATTTATGCAAATAAAAAAAATAAAATCTTTCTATTGTT
*
44080 AAATGTATTAACTATTTATGCAAAT-AGAAAAAT-AAATCTTTCTATTGTT
1 AAATGTATTAACTATTTATGCAAATAAAAAAAATAAAATCTTTCTATTGTT
44129 AAATGTATTA
1 AAATGTATTA
44139 TGAAATGTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
49 26 0.46
50 13 0.23
51 17 0.30
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.41
Consensus pattern (51 bp):
AAATGTATTAACTATTTATGCAAATAAAAAAAATAAAATCTTTCTATTGTT
Found at i:73080 original size:24 final size:22
Alignment explanation
Indices: 73053--73110 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
73043 AAAAAAAATT
*
73053 AAAACTTAAAATAAATAATTTTA
1 AAAAATTAAAATAAAT-ATTTTA
**
73076 AAAAATTCTAAAATTTATATTTTA
1 AAAAA-T-TAAAATAAATATTTTA
73100 AAAAATTAAAA
1 AAAAATTAAAA
73111 AGATCTAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 5 0.17
23 5 0.17
24 12 0.40
25 8 0.27
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAAATTAAAATAAATATTTTA
Found at i:73087 original size:25 final size:24
Alignment explanation
Indices: 73059--73106 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
73049 AATTAAAACT
73059 TAAAATAAATAATTTTAAAAAATTC
1 TAAAATAAAT-ATTTTAAAAAATTC
**
73084 TAAAATTTATATTTTAAAAAATT
1 TAAAATAAATATTTTAAAAAATT
73107 AAAAAGATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAAATAAATATTTTAAAAAATTC
Found at i:73241 original size:16 final size:16
Alignment explanation
Indices: 73222--73252 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
73212 TTGAAAAAAT
73222 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
73238 TTTCAAATTTATATG
1 TTTCAAATATATATG
73253 TTCTAACATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:75444 original size:12 final size:12
Alignment explanation
Indices: 75427--75451 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
75417 CGATAATAAC
75427 ATCTACAAAACA
1 ATCTACAAAACA
75439 ATCTACAAAACA
1 ATCTACAAAACA
75451 A
1 A
75452 CAATAACATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (12 bp):
ATCTACAAAACA
Found at i:76012 original size:195 final size:195
Alignment explanation
Indices: 75633--76068 Score: 547
Period size: 195 Copynumber: 2.2 Consensus size: 195
75623 GATGTTGCTT
* * * * *
75633 ACACGAGCTGTCGAGGACTCGCAACATATGCAATACCCCAACCATCGATACGGTGTCTGTCTATA
1 ACACGAGCTGTCGAGGACTCGCAACATATGCGATACCTCAACCATCGATACGGTATATGTCAATA
* **
75698 TAACTATCTCCTAACGATGCTGCTCACACGAGCTGTCTAGTGTATGCACTTATGCATAAGACTCA
66 TAACTATCTCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCACTTATGCATAAGACTCA
* * ** * *
75763 ACCATCGTAAGGCCTGTAATCTATTCTAGGATTCATATTTTTTTTTCTGACTCACGATGCTACTC
131 ACCATCGTAAGGCCTATAATCCATTCTAGGATTCATATTTCATTTCCCGACTCACGATGCTACTC
* * * * *
75828 ACATGAGCTGTCGAGGACTCGTAACATATGCGGTACCTCAACTATCGATACGGTATATGTGAATA
1 ACACGAGCTGTCGAGGACTCGCAACATATGCGATACCTCAACCATCGATACGGTATATGTCAATA
* * *
75893 TAACTGT-TCCCTAATGATGCTGCTCACATGAGCTGTCGAGAATATGCACTTATGCATAA-ATCT
66 TAACTATCT-CCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCACTTATGCATAAGA-CT
* * * *
75956 CAGCCATCGTAGGGCTTATAATCCATTCTTGGATTC-T-TTACTCATTTCCCGACTCACGATGCT
129 CAACCATCGTAAGGCCTATAATCCATTCTAGGATTCATATT--TCATTTCCCGACTCACGATGCT
*
76019 GCTC
192 ACTC
* *
76023 ACACGAGCTATCGAGGACTTGCAACATATGCGATACCTCAACCATC
1 ACACGAGCTGTCGAGGACTCGCAACATATGCGATACCTCAACCATC
76069 ACGTCTGTTT
Statistics
Matches: 204, Mismatches: 33, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
193 2 0.01
194 3 0.01
195 199 0.98
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (195 bp):
ACACGAGCTGTCGAGGACTCGCAACATATGCGATACCTCAACCATCGATACGGTATATGTCAATA
TAACTATCTCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCACTTATGCATAAGACTCA
ACCATCGTAAGGCCTATAATCCATTCTAGGATTCATATTTCATTTCCCGACTCACGATGCTACTC
Found at i:76572 original size:16 final size:16
Alignment explanation
Indices: 76548--76579 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
76538 TCCTTACAAA
*
76548 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
76564 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
76580 AAAAATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:79140 original size:20 final size:20
Alignment explanation
Indices: 79102--79155 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
79092 AGTCTTCAAG
*
79102 GTATCGATAGAACTAAAGTT
1 GTATCGATAGAAGTAAAGTT
*
79122 GTATCGATAGAAGTGAAGTT
1 GTATCGATAGAAGTAAAGTT
* * *
79142 CTACCAATAGAAGT
1 GTATCGATAGAAGT
79156 CCTAGGACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (20 bp):
GTATCGATAGAAGTAAAGTT
Found at i:96866 original size:26 final size:25
Alignment explanation
Indices: 96810--96869 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
96800 AAGCATACAC
96810 ATTTATATATAATAATACAATAAATT
1 ATTTA-ATATAATAATACAATAAATT
**
96836 A-TTAATATAATTAATACAATTTATT
1 ATTTAATATAA-TAATACAATAAATT
96861 ATTTAATAT
1 ATTTAATAT
96870 TAGAATTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 6 0.20
25 16 0.53
26 8 0.27
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTTAATATAATAATACAATAAATT
Found at i:97309 original size:19 final size:20
Alignment explanation
Indices: 97287--97331 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
97277 TCAAACACTA
97287 AAAAATATCAAAT-TTTTTC
1 AAAAATATCAAATATTTTTC
*
97306 AAAAA-ATCAATTCATTTTTC
1 AAAAATATCAAAT-ATTTTTC
97326 AAAAAT
1 AAAAAT
97332 GAAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.27
19 5 0.23
20 11 0.50
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATATCAAATATTTTTC
Found at i:99620 original size:29 final size:29
Alignment explanation
Indices: 99554--99630 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
99544 TGGCCTAGAC
* *
99554 CGTGTGGCCCACACGGTCTAATACACGAT
1 CGTGTGGCTCACACGGTCTAACACACGAT
99583 CGTGTGGCTCACACGGTCTAACACACGAT
1 CGTGTGGCTCACACGGTCTAACACACGAT
* * *
99612 CGTGGGGCTAACATGGTCT
1 CGTGTGGCTCACACGGTCT
99631 GGCACATGGC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.22, C:0.29, G:0.27, T:0.22
Consensus pattern (29 bp):
CGTGTGGCTCACACGGTCTAACACACGAT
Found at i:103965 original size:4 final size:4
Alignment explanation
Indices: 103958--104013 Score: 67
Period size: 4 Copynumber: 14.0 Consensus size: 4
103948 AAGAATTTAA
* * * *
103958 GTAT GTAT GCAT GCAT GTAT GCAT GTAT GTAT GTAT GTAT GTAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
104006 GCAT GTAT
1 GTAT GTAT
104014 ATTAGAAGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (4 bp):
GTAT
Found at i:103977 original size:12 final size:12
Alignment explanation
Indices: 103960--104013 Score: 81
Period size: 12 Copynumber: 4.5 Consensus size: 12
103950 GAATTTAAGT
103960 ATGTATGCATGC
1 ATGTATGCATGC
*
103972 ATGTATGCATGT
1 ATGTATGCATGC
* *
103984 ATGTATGTATGT
1 ATGTATGCATGC
103996 ATGTATGCATGC
1 ATGTATGCATGC
104008 ATGTAT
1 ATGTAT
104014 ATTAGAAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (12 bp):
ATGTATGCATGC
Found at i:104714 original size:2 final size:2
Alignment explanation
Indices: 104707--104743 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
104697 TATAAAGATT
104707 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
104744 TAAATAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:110262 original size:4 final size:4
Alignment explanation
Indices: 110240--110284 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
110230 CCTATGCATA
* * * *
110240 TATG CATG TATG TAAG TATG TATG TATG TATG TCTG CATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
110285 TCTATGCTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.44
Consensus pattern (4 bp):
TATG
Found at i:118336 original size:12 final size:12
Alignment explanation
Indices: 118321--118369 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
118311 CAACAAAAAT
118321 AACAGCAACAAA
1 AACAGCAACAAA
**
118333 AACAATAACAAA
1 AACAGCAACAAA
* *
118345 AATAGCAGCAAA
1 AACAGCAACAAA
*
118357 AACAGCATCAAA
1 AACAGCAACAAA
118369 A
1 A
118370 TAGTAAAAAC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.65, C:0.20, G:0.08, T:0.06
Consensus pattern (12 bp):
AACAGCAACAAA
Found at i:118337 original size:24 final size:24
Alignment explanation
Indices: 118310--118369 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
118300 AACCAAAACT
118310 ACAACAA-AAATAACAGCAACAAAA
1 ACAACAACAAA-AACAGCAACAAAA
* * *
118334 ACAATAACAAAAATAGCAGCAAAA
1 ACAACAACAAAAACAGCAACAAAA
* *
118358 ACAGCATCAAAA
1 ACAACAACAAAA
118370 TAGTAAAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
24 26 0.90
25 3 0.10
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.07
Consensus pattern (24 bp):
ACAACAACAAAAACAGCAACAAAA
Found at i:118405 original size:21 final size:20
Alignment explanation
Indices: 118340--118405 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 20
118330 AAAAACAATA
**
118340 ACAAAAATAGCAGCAAAAAC
1 ACAAAAATAGCAAAAAAAAC
* *
118360 AGCATCAAAATAGTAAAAACCAAC
1 A-CA--AAAATAGCAAAAA-AAAC
118384 ACAAAAATAGCAAAAAATAAC
1 ACAAAAATAGCAAAAAA-AAC
118405 A
1 A
118406 ATCAAAACAA
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
20 1 0.03
21 18 0.51
23 12 0.34
24 4 0.11
ACGTcount: A:0.65, C:0.18, G:0.08, T:0.09
Consensus pattern (20 bp):
ACAAAAATAGCAAAAAAAAC
Found at i:118441 original size:75 final size:75
Alignment explanation
Indices: 118339--118477 Score: 197
Period size: 75 Copynumber: 1.9 Consensus size: 75
118329 CAAAAACAAT
* * * *
118339 AACAAAAATAGCAGCAAAAACAGCATCAAAATAGTAAAAACCAACACAAAAATAGCAAAAAATAA
1 AACAAAAATAACAGCAAAAACAACATCAAAATAGTAAAAAACAACACAAAAATAACAAAAAATAA
118404 CAATCAAAAC
66 CAATCAAAAC
* ** * *
118414 AACAAAAATAACAGGAAAAGGAACATCAAAATAGTAAAAAACAGCACCAAAATAACAAAAAATA
1 AACAAAAATAACAGCAAAAACAACATCAAAATAGTAAAAAACAACACAAAAATAACAAAAAATA
118478 GCTCCAAAAC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 55 1.00
ACGTcount: A:0.66, C:0.17, G:0.08, T:0.09
Consensus pattern (75 bp):
AACAAAAATAACAGCAAAAACAACATCAAAATAGTAAAAAACAACACAAAAATAACAAAAAATAA
CAATCAAAAC
Found at i:118464 original size:21 final size:21
Alignment explanation
Indices: 118440--118521 Score: 58
Period size: 21 Copynumber: 3.8 Consensus size: 21
118430 AAAGGAACAT
**
118440 CAAAATAGTAAAAAACAGCAC
1 CAAAATAACAAAAAACAGCAC
* *
118461 CAAAATAACAAAAAATAGCTC
1 CAAAATAACAAAAAACAGCAC
* * *
118482 CAAAACAGCAACCAAA-AGACAC
1 CAAAATAACAA-AAAACAG-CAC
*
118504 CAGAAACAACAAAAAACA
1 CA-AAATAACAAAAAACA
118522 ATAATATAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
21 28 0.60
22 10 0.21
23 9 0.19
ACGTcount: A:0.63, C:0.23, G:0.07, T:0.06
Consensus pattern (21 bp):
CAAAATAACAAAAAACAGCAC
Found at i:122137 original size:19 final size:19
Alignment explanation
Indices: 122100--122137 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
122090 AACTTTAATA
*
122100 AATAAAATAAGAATTCTTT
1 AATAAAATAAGAATACTTT
122119 AATATAAATAA-AATACTTT
1 AATA-AAATAAGAATACTTT
122138 CCTTCCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (19 bp):
AATAAAATAAGAATACTTT
Found at i:131089 original size:30 final size:31
Alignment explanation
Indices: 131031--131097 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
131021 TTTGATATTC
* *
131031 AAACTTGACACTTTTTCCTAATTTGGTACCT
1 AAACTTGACAATTTTTCCTAAGTTGGTACCT
* *
131062 AAACTTGACAATTTTT-TTAAGTTGGTACTT
1 AAACTTGACAATTTTTCCTAAGTTGGTACCT
131092 AAACTT
1 AAACTT
131098 TTTGGGGTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.43
Consensus pattern (31 bp):
AAACTTGACAATTTTTCCTAAGTTGGTACCT
Found at i:131113 original size:89 final size:90
Alignment explanation
Indices: 130961--131143 Score: 237
Period size: 89 Copynumber: 2.0 Consensus size: 90
130951 TTAATATAAC
* * * ** *
130961 ATTTGGTACATGAACTTGATACTTTTTCTTATTTTGGTACTTAATATTTTTTGGCTCCAATTTGA
1 ATTTGGTACATAAACTTGACAATTTTTCTTAAGTTGGTACTTAATATTTTTGGGCTCCAATTTGA
131026 TA-TTCAAACTTGACACTTTTTCCTA
66 TACTT-AAACTTGACACTTTTTCCTA
* *
131051 ATTTGGTACCTAAACTTGACAATTTTT-TTAAGTTGGTACTTAA-ACTTTTTGGGGTCCAATTTG
1 ATTTGGTACATAAACTTGACAATTTTTCTTAAGTTGGTACTTAATA-TTTTTGGGCTCCAATTTG
* *
131114 GTACTTAAACTTGACTCTTTTTCCTA
65 ATACTTAAACTTGACACTTTTTCCTA
131140 ATTT
1 ATTT
131144 AGTATGCAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
88 1 0.01
89 55 0.68
90 25 0.31
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.48
Consensus pattern (90 bp):
ATTTGGTACATAAACTTGACAATTTTTCTTAAGTTGGTACTTAATATTTTTGGGCTCCAATTTGA
TACTTAAACTTGACACTTTTTCCTA
Found at i:138619 original size:39 final size:39
Alignment explanation
Indices: 138522--138632 Score: 125
Period size: 39 Copynumber: 2.8 Consensus size: 39
138512 CCTAGCTTCA
* ** *
138522 CAGTGTTTACAGTGTCACCGTCAACTCAGTATTGTATTG
1 CAGTGTTTACAGTGTCACTGTCAGTTCAGTAATGTATTG
* *
138561 CAGTATTTACAGTGGCACTGTCAGTTCAGTAATGTATTG
1 CAGTGTTTACAGTGTCACTGTCAGTTCAGTAATGTATTG
* * *
138600 CAGTGTTTGCAATGTCACTG-CTAGTTTAGTAAT
1 CAGTGTTTACAGTGTCACTGTC-AGTTCAGTAAT
138633 TCGAGAACTT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 1 0.02
39 59 0.98
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (39 bp):
CAGTGTTTACAGTGTCACTGTCAGTTCAGTAATGTATTG
Found at i:138840 original size:73 final size:72
Alignment explanation
Indices: 138738--138941 Score: 209
Period size: 72 Copynumber: 2.8 Consensus size: 72
138728 TTGGCACACG
* * *
138738 CCCGTGCGTCCAGGCCGTGTAACTCACTGTTTCTTATTTCAT-AACACATAATAT-CT-ACACGA
1 CCCGTGTGTCCAGCCCGTGTAACTCACTGTTTCTAATTTC-TCAA-AC--AATATGCTCACACGA
*
138800 T-TGGGCACATA
62 TCT-AGCACATA
* * * *
138811 TCCGTGTGTCCCGCCCGTGTAACTCACTGTTTCTAATTTCTCAAACAATATGCTCACATGGTCTA
1 CCCGTGTGTCCAGCCCGTGTAACTCACTGTTTCTAATTTCTCAAACAATATGCTCACACGATCTA
*
138876 GCACATG
66 GCACATA
* * * *
138883 CCCGTGTGTCCAGCCCGTGTAACTCACTGTTTCTGATTCCTCAAAACAGTATGGTCACA
1 CCCGTGTGTCCAGCCCGTGTAACTCACTGTTTCTAATTTCTC-AAACAATATGCTCACA
138942 TGGCTTAGCA
Statistics
Matches: 111, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
70 5 0.05
71 2 0.02
72 52 0.47
73 52 0.47
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (72 bp):
CCCGTGTGTCCAGCCCGTGTAACTCACTGTTTCTAATTTCTCAAACAATATGCTCACACGATCTA
GCACATA
Found at i:138903 original size:72 final size:72
Alignment explanation
Indices: 138731--138953 Score: 222
Period size: 73 Copynumber: 3.1 Consensus size: 72
138721 ACACGGTTTG
* * * *
138731 GCACACGCCCGTGCGTCCAGGCCGTGTAACTCACTGTTTCTTATTTCAT-AACACATAATAT-CT
1 GCACATGCCCGTGTGTCCAGCCCGTGTAACTCACTGTTTCTAATTTC-TCAA-AC--AATATGCT
* * *
138794 -ACACGAT-TGG
62 CACATGGTCT-A
** *
138804 GCACATATCCGTGTGTCCCGCCCGTGTAACTCACTGTTTCTAATTTCTCAAACAATATGCTCACA
1 GCACATGCCCGTGTGTCCAGCCCGTGTAACTCACTGTTTCTAATTTCTCAAACAATATGCTCACA
138869 TGGTCTA
66 TGGTCTA
* * * *
138876 GCACATGCCCGTGTGTCCAGCCCGTGTAACTCACTGTTTCTGATTCCTCAAAACAGTATGGTCAC
1 GCACATGCCCGTGTGTCCAGCCCGTGTAACTCACTGTTTCTAATTTCTC-AAACAATATGCTCAC
138941 ATGG-CTTA
65 ATGGTC-TA
138949 GCACA
1 GCACA
138954 CACTCATGGG
Statistics
Matches: 127, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
70 5 0.04
71 2 0.02
72 53 0.42
73 67 0.53
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (72 bp):
GCACATGCCCGTGTGTCCAGCCCGTGTAACTCACTGTTTCTAATTTCTCAAACAATATGCTCACA
TGGTCTA
Found at i:138973 original size:73 final size:72
Alignment explanation
Indices: 138824--138975 Score: 164
Period size: 73 Copynumber: 2.1 Consensus size: 72
138814 GTGTGTCCCG
* ** *
138824 CCCGTGTAACTCACTGTTTCTAATTTCTCAAACAATATGCTCACATGGTCTAGCACATGCCCGTG
1 CCCGTGTAACTCACTGTTTCTAATTCCTCAAACAATATGCTCACATGGTCTAGCACACACCCATG
* *
138889 TGTCCAG
66 TGGCCAC
* * * *
138896 CCCGTGTAACTCACTGTTTCTGATTCCTCAAAACAGTATGGTCACATGG-CTTAGCACACACTCA
1 CCCGTGTAACTCACTGTTTCTAATTCCTC-AAACAATATGCTCACATGGTC-TAGCACACACCCA
*
138960 TG-GGCATAC
64 TGTGGC-CAC
138969 CCCGTGT
1 CCCGTGT
138976 GTCTACTATA
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
72 30 0.45
73 36 0.55
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.29
Consensus pattern (72 bp):
CCCGTGTAACTCACTGTTTCTAATTCCTCAAACAATATGCTCACATGGTCTAGCACACACCCATG
TGGCCAC
Found at i:142385 original size:6 final size:7
Alignment explanation
Indices: 142364--142388 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
142354 TGTGTAAGTG
142364 AAATAAA
1 AAATAAA
142371 AAATAAA
1 AAATAAA
142378 AAATAAA
1 AAATAAA
142385 AAAT
1 AAAT
142389 CTTAAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATAAA
Done.