Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011398.1 Kokia drynarioides strain JFW-HI SEQ_126380, 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: 161931
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1762 original size:28 final size:28
Alignment explanation
Indices: 1709--1764 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
1699 CTAGTAACAG
*
1709 GCATGACCTTTGGGTCAACAGGGAGTAA
1 GCATGACCTTTGGGTCAACAGAGAGTAA
*
1737 GCATGACCTTTGGGTCAACATAGAGTAA
1 GCATGACCTTTGGGTCAACAGAGAGTAA
1765 ATCAGATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (28 bp):
GCATGACCTTTGGGTCAACAGAGAGTAA
Found at i:6923 original size:52 final size:52
Alignment explanation
Indices: 6867--7083 Score: 182
Period size: 52 Copynumber: 4.0 Consensus size: 52
6857 CCGGACCTTA
* * *
6867 TAATCCACAAGGGATTCATATACTCACGATGACACAGAGTTATCAGACATCT
1 TAATCCATAAAGGATTCATATACTCACGATGACACAGAGTTATCAGACCTCT
* ** *
6919 TAATCCGTAAAGGATTCATATACTCACGATCTCACGATGACACTTAGTCATCGGACCTCT
1 TAATCCATAAAGGATTCATATACTCACGATGACAC-A-G--AGTTA-TCA---GACCTCT
* * ** * *
6979 TAGTCCATAAAGGATTCATATACTCATGATGACACTTAGTCATCGGACCTCT
1 TAATCCATAAAGGATTCATATACTCACGATGACACAGAGTTATCAGACCTCT
** * ** * *
7031 TAATCTGTAAAGGATTAATATACTCACGATGACACTTAGTCATCAAACCTCT
1 TAATCCATAAAGGATTCATATACTCACGATGACACAGAGTTATCAGACCTCT
7083 T
1 T
7084 CATTTATGGC
Statistics
Matches: 133, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
52 83 0.62
53 1 0.01
54 1 0.01
55 2 0.02
56 7 0.05
57 3 0.02
60 36 0.27
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (52 bp):
TAATCCATAAAGGATTCATATACTCACGATGACACAGAGTTATCAGACCTCT
Found at i:6990 original size:60 final size:60
Alignment explanation
Indices: 6889--7060 Score: 207
Period size: 60 Copynumber: 3.0 Consensus size: 60
6879 GATTCATATA
** * * *
6889 CTCACGATGACACAGAGTTATCAGACATCTTAATCCGTAAAGGATTCATATACTCACGAT
1 CTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGATTCATATACTCACGAT
* *
6949 CTCACGATGACACTTAGTCATCGGACCTCTTAGTCCATAAAGGATTCATATACT--C-A-
1 CTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGATTCATATACTCACGAT
* *
7005 -T---GATGACACTTAGTCATCGGACCTCTTAATCTGTAAAGGATTAATATACTCACGAT
1 CTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGATTCATATACTCACGAT
7061 GACACTTAGT
Statistics
Matches: 97, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
52 45 0.46
54 1 0.01
55 2 0.02
57 1 0.01
58 1 0.01
60 47 0.48
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (60 bp):
CTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGATTCATATACTCACGAT
Found at i:6994 original size:112 final size:112
Alignment explanation
Indices: 6843--7060 Score: 294
Period size: 112 Copynumber: 1.9 Consensus size: 112
6833 TATACTCATA
* *
6843 ATGACACATAGCCACCGGACCTTATAATCCACAAGGGATTCATATACTCACGATGACACAGAGTT
1 ATGACACATAGCCACCGGACCTTATAATCCACAAAGGATTCATATACTCACGATGACACAGAGTC
*
6908 ATCAGACATCTTAATCCGTAAAGGATTCATATACTCACGATCTCACG
66 ATCAGACATCTTAATCCGTAAAGGATTAATATACTCACGATCTCACG
* * * * * * **
6955 ATGACACTTAGTCATCGGACCTCT-TAGTCCATAAAGGATTCATATACTCATGATGACACTTAGT
1 ATGACACATAGCCACCGGACCT-TATAATCCACAAAGGATTCATATACTCACGATGACACAGAGT
* * *
7019 CATCGGACCTCTTAATCTGTAAAGGATTAATATACTCACGAT
65 CATCAGACATCTTAATCCGTAAAGGATTAATATACTCACGAT
7061 GACACTTAGT
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
112 90 0.99
113 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (112 bp):
ATGACACATAGCCACCGGACCTTATAATCCACAAAGGATTCATATACTCACGATGACACAGAGTC
ATCAGACATCTTAATCCGTAAAGGATTAATATACTCACGATCTCACG
Found at i:20856 original size:29 final size:29
Alignment explanation
Indices: 20823--20886 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
20813 AGGGATTAGT
20823 CTTCGCGGTTACATAACGCGTTGTGGGCA
1 CTTCGCGGTTACATAACGCGTTGTGGGCA
20852 CTTCGCGGTTACATAACGCGTTGTGGGCA
1 CTTCGCGGTTACATAACGCGTTGTGGGCA
20881 CTTCGC
1 CTTCGC
20887 ATTGCTTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.28
Consensus pattern (29 bp):
CTTCGCGGTTACATAACGCGTTGTGGGCA
Found at i:23761 original size:15 final size:15
Alignment explanation
Indices: 23721--23766 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
23711 TCAGTCACTT
*
23721 GAAAAAGAA-AAATGA
1 GAAAAAGAAGAAA-AA
23736 GAAAAAGGAAGAAAAA
1 GAAAAA-GAAGAAAAA
23752 GAAAAAGAAGAAAAA
1 GAAAAAGAAGAAAAA
23767 AATTATGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 15 0.54
16 10 0.36
17 3 0.11
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
GAAAAAGAAGAAAAA
Found at i:25593 original size:52 final size:52
Alignment explanation
Indices: 25484--25584 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
25474 AGACGCGATC
* * *
25484 AACCTCTTAATCCGTAAAGGATTCATATACTCATGATGACACTTAGTCAGCG
1 AACCTCGTAATCCATAAAGGATTCATATACTCACGATGACACTTAGTCAGCG
* *
25536 AACCTCGTAATCCATATAGGATTCATATACTTACGATGACACTTAGTCA
1 AACCTCGTAATCCATAAAGGATTCATATACTCACGATGACACTTAGTCA
25585 TTGGACCTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (52 bp):
AACCTCGTAATCCATAAAGGATTCATATACTCACGATGACACTTAGTCAGCG
Found at i:27700 original size:28 final size:28
Alignment explanation
Indices: 27663--27731 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 28
27653 AAATAAGCAT
27663 CATGACCTTTGGGTCAAGAGGGAGAAAG
1 CATGACCTTTGGGTCAAGAGGGAGAAAG
* * *
27691 CATGACCTTTGGGTCAATAGGGGGTAAG
1 CATGACCTTTGGGTCAAGAGGGAGAAAG
27719 CATGACCTTTGGG
1 CATGACCTTTGGG
27732 CCAACATGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.26, C:0.16, G:0.35, T:0.23
Consensus pattern (28 bp):
CATGACCTTTGGGTCAAGAGGGAGAAAG
Found at i:32652 original size:28 final size:28
Alignment explanation
Indices: 32615--32668 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
32605 CTAGTAACAG
32615 GCATGACCTTTGAGTCAACAAGGAGTAA
1 GCATGACCTTTGAGTCAACAAGGAGTAA
* * *
32643 GCATGTCCTTTGGGTCAACATGGAGT
1 GCATGACCTTTGAGTCAACAAGGAGT
32669 GAATCAGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (28 bp):
GCATGACCTTTGAGTCAACAAGGAGTAA
Found at i:37610 original size:28 final size:28
Alignment explanation
Indices: 37572--37626 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
37562 AAATGAGCAT
37572 CATGACCTTTGGGTCAACA-GGTAGTAAG
1 CATGACCTTTGGGTCAACATGG-AGTAAG
37600 CATGACCTTTGGGTCAACATGGAGTAA
1 CATGACCTTTGGGTCAACATGGAGTAA
37627 ATCGGATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (28 bp):
CATGACCTTTGGGTCAACATGGAGTAAG
Found at i:39620 original size:2 final size:2
Alignment explanation
Indices: 39615--39652 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
39605 AAAAAACATC
* *
39615 TA TA TA CA TA CA 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
39653 ATTGACTACT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:42610 original size:36 final size:36
Alignment explanation
Indices: 42563--42660 Score: 151
Period size: 36 Copynumber: 2.7 Consensus size: 36
42553 TGGTAATAGG
*
42563 CATGACCTTTGGGTGAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
*
42599 CATGACCTTTGGGTCAAGAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
* * *
42635 CACGACCTTTGGCTCAACAAGGAGTA
1 CATGACCTTTGGGTCAACAGGGAGTA
42661 TGCATGACCT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
Found at i:46552 original size:23 final size:23
Alignment explanation
Indices: 46520--46573 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
46510 ACGCTACCAC
* *
46520 GCTTATTGTTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTCGTGT
46543 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
46566 GCCTACTG
1 GCTTACTG
46574 ATTTGCGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:46630 original size:23 final size:22
Alignment explanation
Indices: 46532--46632 Score: 78
Period size: 23 Copynumber: 4.5 Consensus size: 22
46522 TTATTGTTTC
* * *
46532 GCACTTTGTGTGCTTACTGTTT
1 GCACTGTGTGTGCCTACTGATT
46554 CGCACT-TCGTGTGCCTACTGATTT
1 -GCACTGT-GTGTGCCTACTGA-TT
** * * *
46578 GCGTTATGTGCGCCTACTAATT
1 GCACTGTGTGTGCCTACTGATT
*
46600 GCAATGTGTGTGCCTACTGGATT
1 GCACTGTGTGTGCCTACT-GATT
46623 GCACTGTGTG
1 GCACTGTGTG
46633 CTTACTATTT
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
22 17 0.27
23 42 0.68
24 3 0.05
ACGTcount: A:0.14, C:0.22, G:0.26, T:0.39
Consensus pattern (22 bp):
GCACTGTGTGTGCCTACTGATT
Found at i:64879 original size:17 final size:17
Alignment explanation
Indices: 64854--64901 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
64844 ACAAATAGAA
64854 TTTTTTTTCTTTTT-TC
1 TTTTTTTTCTTTTTCTC
64870 TTTTTCTTTCTTTTTCTC
1 TTTTT-TTTCTTTTTCTC
*
64888 ATTTTTTTCTTTTT
1 TTTTTTTTCTTTTT
64902 AAGTGACTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 5 0.17
17 18 0.62
18 6 0.21
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTTTCTTTTTCTC
Found at i:65526 original size:17 final size:19
Alignment explanation
Indices: 65482--65518 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
65472 AAATTAACAA
*
65482 AAAAATACAATGACAATAT
1 AAAAATGCAATGACAATAT
65501 AAAAATGCAATGACAATA
1 AAAAATGCAATGACAATA
65519 AAGATGCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.11, G:0.08, T:0.19
Consensus pattern (19 bp):
AAAAATGCAATGACAATAT
Found at i:76783 original size:6 final size:6
Alignment explanation
Indices: 76772--76798 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
76762 GTAAAGACGG
76772 TGGGTA TGGGTA TGGGTA TGGGTA TGG
1 TGGGTA TGGGTA TGGGTA TGGGTA TGG
76799 ACGCTAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.52, T:0.33
Consensus pattern (6 bp):
TGGGTA
Found at i:77367 original size:17 final size:18
Alignment explanation
Indices: 77345--77384 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
77335 AGATTGCATA
77345 CATTTT-TATTGTCATCG
1 CATTTTATATTGTCATCG
* *
77362 CATTTTATTTTGTCATTG
1 CATTTTATATTGTCATCG
77380 CATTT
1 CATTT
77385 CTTTTGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.17, C:0.15, G:0.10, T:0.57
Consensus pattern (18 bp):
CATTTTATATTGTCATCG
Found at i:78003 original size:13 final size:12
Alignment explanation
Indices: 77983--78015 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
77973 AAATATTGAG
77983 AAAAAGAAAAGA
1 AAAAAGAAAAGA
77995 AAAATAGAAAAG-
1 AAAA-AGAAAAGA
78007 AAAAAGAAA
1 AAAAAGAAA
78016 TATTGCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.25
12 8 0.40
13 7 0.35
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:81462 original size:14 final size:15
Alignment explanation
Indices: 81443--81476 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
81433 CCCAATTTTA
*
81443 TTTTTATTTTTA-TT
1 TTTTTAGTTTTAGTT
81457 TTTTTAGTTTTAGTT
1 TTTTTAGTTTTAGTT
81472 TTTTT
1 TTTTT
81477 CCTGCACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTTTAGTTTTAGTT
Found at i:86463 original size:18 final size:19
Alignment explanation
Indices: 86440--86475 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
86430 GTCAATAATT
86440 TGTT-AAGGGTTAACAATA
1 TGTTAAAGGGTTAACAATA
*
86458 TGTTAAAGGTTTAACAAT
1 TGTTAAAGGGTTAACAAT
86476 TGAATGATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (19 bp):
TGTTAAAGGGTTAACAATA
Found at i:93141 original size:25 final size:25
Alignment explanation
Indices: 93112--93166 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
93102 ATATCAGAAT
93112 GGCCACAAGTTTGATATAGAATTGC
1 GGCCACAAGTTTGATATAGAATTGC
*
93137 GGCCACAAGTTTGATTTAGAATTGC
1 GGCCACAAGTTTGATATAGAATTGC
93162 GGCCA
1 GGCCA
93167 AAGATGTCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (25 bp):
GGCCACAAGTTTGATATAGAATTGC
Found at i:94503 original size:18 final size:17
Alignment explanation
Indices: 94478--94511 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
94468 TATTCTTTTT
94478 CTAACTTTTATTGATTA
1 CTAACTTTTATTGATTA
*
94495 CTAATCTTTTGTTGATT
1 CTAA-CTTTTATTGATT
94512 TTCTTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (17 bp):
CTAACTTTTATTGATTA
Found at i:104855 original size:19 final size:20
Alignment explanation
Indices: 104831--104873 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
104821 ACTTGAGATG
104831 TATTG-TATGATGTGATAAA
1 TATTGTTATGATGTGATAAA
*
104850 TATTGTTATGATTTGATAAA
1 TATTGTTATGATGTGATAAA
104870 TATT
1 TATT
104874 TTTCTAATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (20 bp):
TATTGTTATGATGTGATAAA
Found at i:107115 original size:12 final size:13
Alignment explanation
Indices: 107095--107128 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
107085 GAAGAAAAGG
107095 AAAGTAAGATTG-A
1 AAAG-AAGATTGAA
107108 AAAGAAGATTGAA
1 AAAGAAGATTGAA
107121 AAAGAAGA
1 AAAGAAGA
107129 AAGTGATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.15
Consensus pattern (13 bp):
AAAGAAGATTGAA
Found at i:107878 original size:214 final size:215
Alignment explanation
Indices: 107470--108331 Score: 833
Period size: 213 Copynumber: 4.0 Consensus size: 215
107460 TTCACAAAAC
* * * * *
107470 GACAAGCCTCAACTATTTAGACCAAATGATGCGACTTTCT-AAGTATGGAATGTTTGAAAAATTG
1 GACAAGCTTAAACTATTTAGACCAAATGATGCGA-TTTCTCGAGCATGAAATGTTTGAAAAATTG
* * * *
107534 CTCGAAAGAATGGATCGTCATGAATACATTAAGGAACATAAGTTATAAAAGAACTCGTAAAAGTT
65 CTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACA-AAGTTATAAAAGAACTCGTAAAAGTT
* * * * * * * * * *
107599 TGATAAGTTTGAAAGTTCAGTCAAGAACCTACAGAGAAATACTTCTTA-AGTACATAATA-TTTA
129 TGACAAGTTCGAAAGTTCGGTCAAGAACCAAGAGAGAAACAATTCTCATA-TAAATAAGATTTTA
107662 ATTCAAAGACCAAAAGTTGTT-T
193 ATTCAAAGACCAAAAGTTGTTAT
* * * * *
107684 -ACAAGCTTAAACTATTTAGACCAAATAATGCAATCTC-CTGAGCATTAAATGTTTTGGAAAATT
1 GACAAGCTTAAACTATTTAGACCAAATGATGCGATTTCTC-GAGCATGAAATG-TTTGAAAAATT
* * * * *
107747 GTTCGAAGGAATGGATCATCTTGAATATTTTAAGGAACCAAAGTTATAAAACAATTCATAAAAGT
64 GCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAA-CAAAGTTATAAAAGAACTCGTAAAAGT
* * *
107812 TTGACAACTTCG-AAGTTCGGTCAATAACCAAGAGAGAAACAATTCTCACATAAATAAGATTTTA
128 TTGACAAGTTCGAAAGTTCGGTCAAGAACCAAGAGAGAAACAATTCTCATATAAATAAGATTTTA
* *
107876 ATTCAAAAACCAAAAGTTATTTTCATAAT
193 ATTCAAAGACCAAAAG---TTGT--T-AT
* * * * * *
107905 GACAAGCTTAAAATATTTAGACCAAATGATGCGATTTTTCAAGCAAGAAATGTTCGAAAAATTGG
1 GACAAGCTTAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGAAATGTTTGAAAAATTGC
* * *
107970 TCGAAGG--T--ATGA---T-AATTCTTTAAGGAAACGAAGTTATAAAAGAACTCGTAAAAGTTT
66 TCGAAGGAATGGATCATCTTGAATACTTTAAGG-AACAAAGTTATAAAAGAACTCGTAAAAGTTT
* * * *
108027 GACAAGTTCGAAAGTTCGATTAAGAACCAAGAGAGAAACAATTCCCATGTAAATAAG-TTTCTAA
130 GACAAGTTCGAAAGTTCGGTCAAGAACCAAGAGAGAAACAATTCTCATATAAATAAGATTT-TAA
108091 TTCAAAGA-CAAAAGTTGTTTACAAAAT
194 TTCAAAGACCAAAAGTTG-TT-----AT
* * *
108118 GACAAGCTTAAACTATTTAGAACAAATGATGCGATTTCTCGAGCATGGAATGTTTTG-AAACTTG
1 GACAAGCTTAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGAAATG-TTTGAAAAATTG
* * * *
108182 CTCGAAGGTATGGATCATCTTGAATACTTTAAGGAATCGAAGTTAAAAAATAACTCGTAAAAGTT
65 CTCGAAGGAATGGATCATCTTGAATACTTTAAGGAA-CAAAGTTATAAAAGAACTCGTAAAAGTT
* * * * * * * *
108247 TGATAAGTTCAAAAGTTTGGTAAAGAACCAAGAGAGAAACAATTCTAATGTAAATATGTTTTTAA
129 TGACAAGTTCGAAAGTTCGGTCAAGAACCAAGAGAGAAACAATTCTCATATAAATAAGATTTTAA
*
108312 TTCAAAGATCAAAAGTTGTT
194 TTCAAAGACCAAAAGTTGTT
108332 TACAAAAGTT
Statistics
Matches: 532, Mismatches: 81, Indels: 63
0.79 0.12 0.09
Matches are distributed among these distances:
209 1 0.00
210 2 0.00
211 1 0.00
212 3 0.01
213 188 0.35
214 148 0.28
215 3 0.01
217 9 0.02
219 2 0.00
220 3 0.01
221 118 0.22
222 53 0.10
223 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (215 bp):
GACAAGCTTAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGAAATGTTTGAAAAATTGC
TCGAAGGAATGGATCATCTTGAATACTTTAAGGAACAAAGTTATAAAAGAACTCGTAAAAGTTTG
ACAAGTTCGAAAGTTCGGTCAAGAACCAAGAGAGAAACAATTCTCATATAAATAAGATTTTAATT
CAAAGACCAAAAGTTGTTAT
Found at i:109044 original size:10 final size:10
Alignment explanation
Indices: 109022--109076 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
109012 TAACTTACAA
109022 CACATATTAAT
1 CACATA-TAAT
109033 CACATATAAT
1 CACATATAAT
*
109043 CACATACAAT
1 CACATATAAT
* * *
109053 CATATTTAGT
1 CACATATAAT
*
109063 CACATTTAAT
1 CACATATAAT
109073 CACA
1 CACA
109077 ATTTATGACA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
10 31 0.84
11 6 0.16
ACGTcount: A:0.44, C:0.22, G:0.02, T:0.33
Consensus pattern (10 bp):
CACATATAAT
Found at i:109051 original size:30 final size:30
Alignment explanation
Indices: 109017--109076 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
109007 AAGCATAACT
109017 TACAACACATA-TTAATCACATATAATCACA
1 TACAA-ACATATTTAATCACATATAATCACA
* * *
109047 TACAATCATATTTAGTCACATTTAATCACA
1 TACAAACATATTTAATCACATATAATCACA
109077 ATTTATGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.32
Consensus pattern (30 bp):
TACAAACATATTTAATCACATATAATCACA
Found at i:109556 original size:36 final size:35
Alignment explanation
Indices: 109479--109556 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 35
109469 AAGATAATCA
*
109479 TTCACATGGCATGAAAAACATACCCACATATTTAT
1 TTCACATGGCATGAAAAACATACCCACATATTCAT
* *
109514 TGTCACATGGCATGAATAACATACCCTCATATTCACT
1 T-TCACATGGCATGAAAAACATACCCACATATTCA-T
109551 TTCACA
1 TTCACA
109557 GCAGTTCTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 1 0.03
36 35 0.92
37 2 0.05
ACGTcount: A:0.36, C:0.26, G:0.09, T:0.29
Consensus pattern (35 bp):
TTCACATGGCATGAAAAACATACCCACATATTCAT
Found at i:114853 original size:26 final size:27
Alignment explanation
Indices: 114805--114859 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
114795 AATCATTGGA
114805 AAAATAAGATTAATTTAAAATACAAAG
1 AAAATAAGATTAATTTAAAATACAAAG
* * *
114832 AAAATAA-TTTAATTTTATATACAAAG
1 AAAATAAGATTAATTTAAAATACAAAG
114858 AA
1 AA
114860 TCGAAAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.31
Consensus pattern (27 bp):
AAAATAAGATTAATTTAAAATACAAAG
Found at i:114946 original size:30 final size:30
Alignment explanation
Indices: 114907--114965 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
114897 GAAGTTTTGG
* *
114907 GGGTTAAAATGTAATTTTAGAAAAATTTTA
1 GGGTCAAAATATAATTTTAGAAAAATTTTA
* *
114937 GGGTCAAAATATAATTTTTGGAAAATTTT
1 GGGTCAAAATATAATTTTAGAAAAATTTT
114966 GGAAATTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.41
Consensus pattern (30 bp):
GGGTCAAAATATAATTTTAGAAAAATTTTA
Found at i:115052 original size:30 final size:30
Alignment explanation
Indices: 115006--115162 Score: 131
Period size: 30 Copynumber: 5.3 Consensus size: 30
114996 GAAAGTTTAG
* * *
115006 GGGTCAAATTTGAATTTTTGGGAAGTTCGA
1 GGGTCAAATCTAAATTTTTAGGAAGTTCGA
* * * * *
115036 GGGTTAAATCCAAATTTTTAAGAAGTTTTGG
1 GGGTCAAATCTAAATTTTTAGGAAG-TTCGA
* * *
115067 GGGTCAAATCTGAATTTTT-TGATGTTC-A
1 GGGTCAAATCTAAATTTTTAGGAAGTTCGA
* * * *
115095 GAGTTAAAACTTAATTTTT-GGAAAGTTCGA
1 GGGTCAAATCTAAATTTTTAGG-AAGTTCGA
*
115125 GGGTCAAATCTAAATTTTTAGAAAGTTCGA
1 GGGTCAAATCTAAATTTTTAGGAAGTTCGA
115155 GGGTCAAA
1 GGGTCAAA
115163 ACAATTTTTG
Statistics
Matches: 97, Mismatches: 26, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
28 16 0.16
29 7 0.07
30 54 0.56
31 20 0.21
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (30 bp):
GGGTCAAATCTAAATTTTTAGGAAGTTCGA
Found at i:115122 original size:29 final size:29
Alignment explanation
Indices: 114962--115179 Score: 124
Period size: 30 Copynumber: 7.4 Consensus size: 29
114952 TTTTGGAAAA
* * *
114962 TTTTGGAAATTTTG-GGGCCAAAACATAAT
1 TTTTGGAAAGTTCGAGGGTCAAAAC-TAAT
* **
114991 TTTTGGAAAGTT-TAGGGGTCAAATTTGAAT
1 TTTTGGAAAGTTCGA-GGGTCAAAACT-AAT
* * * *
115021 TTTTGGGAAGTTCGAGGGTTAAATCCAAAT
1 TTTTGGAAAGTTCGAGGGTCAAA-ACTAAT
* * * *
115051 TTTT-AAGAAGTTTTGGGGGTCAAATCTGAAT
1 TTTTGGA-AAG-TTCGAGGGTCAAAACT-AAT
* * * *
115082 TTTTTG-ATGTTC-AGAGTTAAAACTTAAT
1 TTTTGGAAAGTTCGAGGGTCAAAAC-TAAT
*
115110 TTTTGGAAAGTTCGAGGGTCAAATCTAAAT
1 TTTTGGAAAGTTCGAGGGTCAAAACT-AAT
*
115140 TTTTAGAAAGTTCGAGGGTCAAAAC-AAT
1 TTTTGGAAAGTTCGAGGGTCAAAACTAAT
*
115168 TTTTGGACAGTT
1 TTTTGGAAAGTT
115180 TGGGTTTCAA
Statistics
Matches: 142, Mismatches: 34, Indels: 27
0.70 0.17 0.13
Matches are distributed among these distances:
28 28 0.20
29 21 0.15
30 75 0.53
31 18 0.13
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (29 bp):
TTTTGGAAAGTTCGAGGGTCAAAACTAAT
Found at i:127978 original size:20 final size:21
Alignment explanation
Indices: 127953--127992 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
127943 TGCATATTTA
127953 TCATTTT-TAACTTAGTGATT
1 TCATTTTCTAACTTAGTGATT
127973 TCATTTTCTAACTTAGTGAT
1 TCATTTTCTAACTTAGTGAT
127993 GCTCGATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (21 bp):
TCATTTTCTAACTTAGTGATT
Found at i:129381 original size:2 final size:2
Alignment explanation
Indices: 129374--129404 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
129364 AGGGACGGAA
*
129374 AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
129405 TTAGATTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:132712 original size:41 final size:41
Alignment explanation
Indices: 132647--132727 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
132637 AAAGGCAAAG
* *
132647 GGTTAATATATATGTAGAGTGAGAGATTAGATGAATATTAT
1 GGTTAATATATATGTAGAGGGAGAGATTAGATAAATATTAT
*
132688 GGTTAATATATCT-TGAGAGGGAGAGATTAGATAAATATTA
1 GGTTAATATATATGT-AGAGGGAGAGATTAGATAAATATTA
132728 GATAAACTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.03
41 35 0.97
ACGTcount: A:0.40, C:0.01, G:0.25, T:0.35
Consensus pattern (41 bp):
GGTTAATATATATGTAGAGGGAGAGATTAGATAAATATTAT
Found at i:132739 original size:41 final size:41
Alignment explanation
Indices: 132662--132739 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
132652 ATATATATGT
* * * *
132662 AGAGTGAGAGATTAGATGAATATTATGGTTAATATATCTTG
1 AGAGGGAGAGATTAGATAAATATTATGATAAATATATCTTG
132703 AGAGGGAGAGATTAGATAAATATTA-GATAAACTATAT
1 AGAGGGAGAGATTAGATAAATATTATGATAAA-TATAT
132740 ATTACACTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 4 0.12
41 28 0.88
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.32
Consensus pattern (41 bp):
AGAGGGAGAGATTAGATAAATATTATGATAAATATATCTTG
Found at i:135820 original size:2 final size:2
Alignment explanation
Indices: 135813--135840 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
135803 TTTGGTACTC
135813 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
135841 TCATTTAATT
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:137047 original size:30 final size:30
Alignment explanation
Indices: 137011--137077 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
137001 TGTTCCTAGT
*
137011 CCAAGAATACAAATTATGGTCTTCTTTTCA
1 CCAAGAATACAAATTACGGTCTTCTTTTCA
* * *
137041 CCAAGAATACCACTTACGGTCTTCTTTTGA
1 CCAAGAATACAAATTACGGTCTTCTTTTCA
137071 CCAAGAA
1 CCAAGAA
137078 GATCCATGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (30 bp):
CCAAGAATACAAATTACGGTCTTCTTTTCA
Found at i:138327 original size:41 final size:41
Alignment explanation
Indices: 138269--138380 Score: 134
Period size: 41 Copynumber: 2.7 Consensus size: 41
138259 CCAAAGCCAA
* * *
138269 ATGATTAATATTAATTGAGAGTGAGAGATTAGATGAAGACT
1 ATGATTAATATTTATTGAGAGTGAGAGAGTAGATAAAGACT
* * *
138310 ATGATTAATATTTATTGAGAGTGGGAGAGTATATAAAGAGT
1 ATGATTAATATTTATTGAGAGTGAGAGAGTAGATAAAGACT
* * * *
138351 ATGAGTAATATATATGGAGAGTTAGAGAGT
1 ATGATTAATATTTATTGAGAGTGAGAGAGT
138381 GAAAGATTAG
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.40, C:0.01, G:0.27, T:0.32
Consensus pattern (41 bp):
ATGATTAATATTTATTGAGAGTGAGAGAGTAGATAAAGACT
Found at i:139616 original size:41 final size:46
Alignment explanation
Indices: 139556--139672 Score: 163
Period size: 49 Copynumber: 2.6 Consensus size: 46
139546 TCAAATCCAA
139556 ATAATTAATATATATGGAGAGTGAGAGA-T-T-AGA-AG-AAGACT
1 ATAATTAATATATATGGAGAGTGAGAGAGTCTAAGATAGTAAGACT
*
139597 ATGATTAATATATATGGAGAGTGAGAGAGTCTAAGATTAGATTAAGACT
1 ATAATTAATATATATGGAGAGTGAGAGAGTCTAAGA-TAG--TAAGACT
139646 ATAATTAATATATATGGAGAGTGAGAG
1 ATAATTAATATATATGGAGAGTGAGAG
139673 GGTGAGAGAT
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
41 27 0.41
42 1 0.02
43 1 0.02
44 3 0.05
46 2 0.03
49 32 0.48
ACGTcount: A:0.44, C:0.03, G:0.25, T:0.29
Consensus pattern (46 bp):
ATAATTAATATATATGGAGAGTGAGAGAGTCTAAGATAGTAAGACT
Found at i:139683 original size:49 final size:49
Alignment explanation
Indices: 139572--139695 Score: 178
Period size: 49 Copynumber: 2.5 Consensus size: 49
139562 AATATATATG
* *
139572 GAGAGTGAGAGATTAGAAGAAGACTATGATTAATATATATGGAGAGTGA
1 GAGAGTGAGAGATTAGATGAAGACTATAATTAATATATATGGAGAGTGA
* *
139621 GAGAGTCTA-AGATTAGATTAAGACTATAATTAATATATATGGAGAGTGA
1 GAGAGT-GAGAGATTAGATGAAGACTATAATTAATATATATGGAGAGTGA
* *
139670 GAGGGTGAGAGATTAGATGAATACTA
1 GAGAGTGAGAGATTAGATGAAGACTA
139696 GAAAAAACAT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
48 1 0.02
49 63 0.97
50 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.28, T:0.27
Consensus pattern (49 bp):
GAGAGTGAGAGATTAGATGAAGACTATAATTAATATATATGGAGAGTGA
Found at i:143671 original size:801 final size:802
Alignment explanation
Indices: 142131--143745 Score: 2937
Period size: 801 Copynumber: 2.0 Consensus size: 802
142121 GACTATCCAC
*
142131 AAAAGCAGTTAAGGATCAAACACCCTTTGAGGCTTCGTATGGTCATAAACCATCTTTAAATTTTC
1 AAAAGCAATTAAGGATCAAACACCCTTTGAGGCTTCGTATGGTCATAAACCATCTTTAAATTTTC
142196 TCAAAATATTTGGTTGTTTGTACTTAACTCATGTTCTAATAATCAAGAGAGTAGTTCGTTATATC
66 TCAAAATATTTGGTTGTTTGTACTTAACTCATGTTCTAATAATCAAGAGAGTAGTTCGTTATATC
142261 AAAGGCACCGATAATTTTGGTGTTAAATTCAAAAGAGGCAAGGAGTTCAACCTTGTTGGCTTCTC
131 AAAGGCACCGATAATTTTGGTGTTAAATTCAAAAGAGGCAAGGAGTTCAACCTTGTTGGCTTCTC
*
142326 TGATATTGATTGGTGAGGTTTCATTAATGACATGAGGAGTACATCAAGCTATTGTTTTACTTTTG
196 TGATATTGATTGGGGAGGTTTCATTAATGACATGAGGAGTACATCAAGCTATTGTTTTACTTTTG
*
142391 ATCTGGTGTCTTCTCATGGAGCTCGAAGAAGCAAGAAACTGTTGCTCAATCTACTGTTGAAGCAG
261 ATCTGGTGTCTTCTCATGGAGCTCGAAGAAGCAAGAAACTGTTGCTCAATCTACTGTTGAAGCAA
* *
142456 AATTTGTTGCTGCAGCAGTCGCTGTTAATCATGCTTTGTGGTTGAGAAAATTATTAAGTGATCTT
326 AATTTGTTGCTACAGCAGTCGCTGTTAATCATGCTTTGTGGTTGAGAAAATTATTAAATGATCTT
*
142521 AACCTTGAACAGAAGGAAAGCACAATGATTTTCATTAATAATCAAGCTGCCATTACAATTTCTCA
391 AACCTTGAACAGAAGGAAAGCACAATGATTTTCATTAATAATCAAGCTGCCATTACAATTTCTAA
* *
142586 TGATCCAGTATTTCATGGGAAGACTAAGCATTTCAATATTAAGCTTTTCTTTTTGAGGGAAGTGC
456 TAATCCAGTATTTCATGGGAAGACTAAGCATTTCAATATTAAGCTTTTCTTTTTGAGGGAACTGC
142651 AAAAAGAATGTAACGTTATACTAGTTCATTGCAAAACAGAGAAGAAGGTTGAAGATATCTTCACC
521 AAAAAGAATGTAACGTTATACTAGTTCATTGCAAAACAGAGAAGAAGGTTGAAGATATCTTCACC
*
142716 ATGCCGCTCCTCGTAAGCAAATTTGGAGTTTTGAGAACAACACTTGGTGTTTGCAACAATTGAAG
586 ATGCCGCTCCTAGTAAGCAAATTTGGAGTTTTGAGAACAACACTTGGTGTTTGCAACAATTGAAG
142781 CAAGGAGTGCTGAAGATTTGCTTCAACTATCATAATCTAGCTAATTTTAGATATAATCATAGCTC
651 CAAGGAGTGCTGAAGATTTGCTTCAACTATCATAATCTAGCTAATTTTAGATATAATCATAGCTC
142846 TTTAATTTGTTCC-AGATT-TTTTAGAGATTATGTTTCTATTAGTAGCCTATTTTTAGTTAGTAG
716 TTTAATTTGTTCCTAGATTCTTTTAGAGATTATGTTTCTATTAGTAGCCTATTTTTAGTTAGTAG
142909 TTGTTAACTTGTTTACTATATA
781 TTGTTAACTTGTTTACTATATA
* *
142931 AAAAGCAATTATGGATCAAACACCCTTTGAGGCTTGGTATGGTCATAAACCATCTTTAAATTTTC
1 AAAAGCAATTAAGGATCAAACACCCTTTGAGGCTTCGTATGGTCATAAACCATCTTTAAATTTTC
142996 TCAAAATATTTGGTTGTTTGTACTTAACTCATGTTCTAATAATCAAGAGAGTAGTTCGTTATATC
66 TCAAAATATTTGGTTGTTTGTACTTAACTCATGTTCTAATAATCAAGAGAGTAGTTCGTTATATC
143061 AAAGGCACCGATAATTTTGGTGTTAAATTCAAAAGAGGCAAGGAGTTCAACCTTGTTGGCTTCTC
131 AAAGGCACCGATAATTTTGGTGTTAAATTCAAAAGAGGCAAGGAGTTCAACCTTGTTGGCTTCTC
143126 TGATATTGATTGGGGAGGTTTCATTAATGACATGAGGAGTACATCAAGCTATTGTTTTACTTTTT
196 TGATATTGATTGGGGAGGTTTCATTAATGACATGAGGAGTACATCAAGCTATTGTTTTAC-TTTT
* *
143191 GATTTGGTGTCTTCTCATGGAGCTCGAAGAAGCAAGAAATTGTTGCTCAATCTACTGTTGAAGCA
260 GATCTGGTGTCTTCTCATGGAGCTCGAAGAAGCAAGAAACTGTTGCTCAATCTACTGTTGAAGCA
143256 AAATTTGTTGCTACAGCAGTCGCTGTTAATCATGCTTTGTGGTTGAGAAAATTATTAAATGATCT
325 AAATTTGTTGCTACAGCAGTCGCTGTTAATCATGCTTTGTGGTTGAGAAAATTATTAAATGATCT
143321 TAACCTTGAACAGAAGGAAAGCACAATGATTTTCATTAATAATCAAGCTGCCATTACAATTTCTA
390 TAACCTTGAACAGAAGGAAAGCACAATGATTTTCATTAATAATCAAGCTGCCATTACAATTTCTA
* * *
143386 ATAATCTAGTATTTCATGGGAAGACTAAGTATTTCAATATTAAGCTTTTCTTTTTTAGGGAACTG
455 ATAATCCAGTATTTCATGGGAAGACTAAGCATTTCAATATTAAGCTTTTCTTTTTGAGGGAACTG
*
143451 CAAAAAGAATGTAACGTTATACTAGTTCATTGCAAAATAGAGAAGAAGGTTGAAGATATCTTCAC
520 CAAAAAGAATGTAACGTTATACTAGTTCATTGCAAAACAGAGAAGAAGGTTGAAGATATCTTCAC
143516 CATGCCGCTCCTAGTAAGCAAATTTGGAGTTTTGAGAACAACACTTGGTGTTTGCAACAATTGAA
585 CATGCCGCTCCTAGTAAGCAAATTTGGAGTTTTGAGAACAACACTTGGTGTTTGCAACAATTGAA
**
143581 GCAAGGAGTGCTGAAGATTTGCTTCAGTTATCATAATCTAGCTAATTTTAGATATAATCATAGCT
650 GCAAGGAGTGCTGAAGATTTGCTTCAACTATCATAATCTAGCTAATTTTAGATATAATCATAGCT
*
143646 CTTTAATTTGTTCCAGATTTTTTAGAGATTCTTTTAGAGATTATGTTTCTGTTAGTAGCCTATTT
715 CTTTAATTTGTTCC--------T--AGATTCTTTTAGAGATTATGTTTCTATTAGTAGCCTATTT
143711 TTAGTTAGTAGTTGTTAACTTGTTTACTATATA
770 TTAGTTAGTAGTTGTTAACTTGTTTACTATATA
143744 AA
1 AA
143746 CACTAGTTTC
Statistics
Matches: 782, Mismatches: 20, Indels: 13
0.96 0.02 0.02
Matches are distributed among these distances:
800 251 0.32
801 458 0.59
812 5 0.01
813 68 0.09
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (802 bp):
AAAAGCAATTAAGGATCAAACACCCTTTGAGGCTTCGTATGGTCATAAACCATCTTTAAATTTTC
TCAAAATATTTGGTTGTTTGTACTTAACTCATGTTCTAATAATCAAGAGAGTAGTTCGTTATATC
AAAGGCACCGATAATTTTGGTGTTAAATTCAAAAGAGGCAAGGAGTTCAACCTTGTTGGCTTCTC
TGATATTGATTGGGGAGGTTTCATTAATGACATGAGGAGTACATCAAGCTATTGTTTTACTTTTG
ATCTGGTGTCTTCTCATGGAGCTCGAAGAAGCAAGAAACTGTTGCTCAATCTACTGTTGAAGCAA
AATTTGTTGCTACAGCAGTCGCTGTTAATCATGCTTTGTGGTTGAGAAAATTATTAAATGATCTT
AACCTTGAACAGAAGGAAAGCACAATGATTTTCATTAATAATCAAGCTGCCATTACAATTTCTAA
TAATCCAGTATTTCATGGGAAGACTAAGCATTTCAATATTAAGCTTTTCTTTTTGAGGGAACTGC
AAAAAGAATGTAACGTTATACTAGTTCATTGCAAAACAGAGAAGAAGGTTGAAGATATCTTCACC
ATGCCGCTCCTAGTAAGCAAATTTGGAGTTTTGAGAACAACACTTGGTGTTTGCAACAATTGAAG
CAAGGAGTGCTGAAGATTTGCTTCAACTATCATAATCTAGCTAATTTTAGATATAATCATAGCTC
TTTAATTTGTTCCTAGATTCTTTTAGAGATTATGTTTCTATTAGTAGCCTATTTTTAGTTAGTAG
TTGTTAACTTGTTTACTATATA
Found at i:145350 original size:27 final size:27
Alignment explanation
Indices: 145320--145374 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
145310 ATAGACCCTT
145320 ATCATATCTGATATTGTAGCTATTCAC
1 ATCATATCTGATATTGTAGCTATTCAC
* * * *
145347 ATCATGTTTGATATTGTAGTTGTTCAC
1 ATCATATCTGATATTGTAGCTATTCAC
145374 A
1 A
145375 ATTTCTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (27 bp):
ATCATATCTGATATTGTAGCTATTCAC
Found at i:149703 original size:23 final size:23
Alignment explanation
Indices: 149679--150106 Score: 500
Period size: 23 Copynumber: 18.6 Consensus size: 23
149669 CTTGTATCTA
* * *
149679 TGCTTATATATTATTATGATTTA
1 TGCTTAAATATTAATATGATTTG
* *
149702 TGCTTAAATGTTAATATGATTTA
1 TGCTTAAATATTAATATGATTTG
* * *
149725 TCCTTAAATATTAATTTGATTTA
1 TGCTTAAATATTAATATGATTTG
*
149748 TGCTTAAATATT-ATAGTGATTTA
1 TGCTTAAATATTAATA-TGATTTG
* *
149771 TGCTTAAATGTTAATATGATTTA
1 TGCTTAAATATTAATATGATTTG
* *
149794 TGCTTAAATACTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
* *
149817 TGTTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
*
149840 TTCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* *
149863 TTCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
*
149886 TGCTTAAATATTAATCTGATTTG
1 TGCTTAAATATTAATATGATTTG
* * *
149909 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATATGATTTG
* *
149932 TGCTTAAATATTAGTGTGATTTG
1 TGCTTAAATATTAATATGATTTG
* *
149955 T-CTTTAAATATTAATGTTATTTG
1 TGC-TTAAATATTAATATGATTTG
* * * *
149978 TGCTTAAGTGTTAAGATGATTTA
1 TGCTTAAATATTAATATGATTTG
150001 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* *
150024 TGCTCAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
*
150047 TACTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* * *
150070 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATATGATTTG
150093 TGCTTAAATATTAA
1 TGCTTAAATATTAA
150107 GTTGTGATAT
Statistics
Matches: 352, Mismatches: 49, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
22 3 0.01
23 345 0.98
24 4 0.01
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (23 bp):
TGCTTAAATATTAATATGATTTG
Found at i:149788 original size:69 final size:69
Alignment explanation
Indices: 149679--150106 Score: 563
Period size: 69 Copynumber: 6.2 Consensus size: 69
149669 CTTGTATCTA
* * * * * * *
149679 TGCTTATATATTATTATGATTTATGCTTAAATGTTAATATGATTTATCCTTAAATATTAATTTGA
1 TGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTGA
*
149744 TTTA
66 TTTG
* * *
149748 TGCTTAAATATT-ATAGTGATTTATGCTTAAATGTTAATATGATTTATGCTTAAATACTAATGTG
1 TGCTTAAATATTAAT-GTGATTTGTGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTG
149812 ATTTG
65 ATTTG
* * * *
149817 TGTTTAAATATTAATGTGATTTGTTCTTAAATATTAATATGATTTGTTCTTAAATATTAATGTGA
1 TGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTGA
149882 TTTG
66 TTTG
* * * *
149886 TGCTTAAATATTAATCTGATTTGTGCTCAAATATTAATGTGATTTATGCTTAAATATTAGTGTGA
1 TGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTGA
149951 TTTG
66 TTTG
* * * * *
149955 T-CTTTAAATATTAATGTTATTTGTGCTTAAGTGTTAAGATGATTTATGCTTAAATATTAATATG
1 TGC-TTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTG
150019 ATTTG
65 ATTTG
* * * *
150024 TGCTCAAATATTAATGTGATTTGTACTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGA
1 TGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTGA
*
150089 TTTA
66 TTTG
150093 TGCTTAAATATTAA
1 TGCTTAAATATTAA
150107 GTTGTGATAT
Statistics
Matches: 313, Mismatches: 42, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
68 2 0.01
69 308 0.98
70 3 0.01
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (69 bp):
TGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTGA
TTTG
Found at i:151292 original size:25 final size:23
Alignment explanation
Indices: 151251--151296 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
151241 CCAATTAGGG
151251 AATTATTCTTTAGATTTAATTCT
1 AATTATTCTTTAGATTTAATTCT
*
151274 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TCTTTAG-ATTTAATT
151297 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.57
Consensus pattern (23 bp):
AATTATTCTTTAGATTTAATTCT
Found at i:152414 original size:13 final size:13
Alignment explanation
Indices: 152345--152415 Score: 54
Period size: 13 Copynumber: 5.4 Consensus size: 13
152335 TAATTTAGCC
152345 ATTTTTTAATTTT
1 ATTTTTTAATTTT
* *
152358 ATTTTCATAGTTTT
1 ATTTT-TTAATTTT
* *
152372 AGTTTTTAA-TAT
1 ATTTTTTAATTTT
* *
152384 AATTTTTACATTTA
1 ATTTTTTA-ATTTT
*
152398 ATTTTTTTATTTT
1 ATTTTTTAATTTT
152411 ATTTT
1 ATTTT
152416 ATAGGTTCTT
Statistics
Matches: 43, Mismatches: 12, Indels: 6
0.70 0.20 0.10
Matches are distributed among these distances:
12 9 0.21
13 17 0.40
14 17 0.40
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (13 bp):
ATTTTTTAATTTT
Found at i:155529 original size:15 final size:16
Alignment explanation
Indices: 155511--155552 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
155501 AAACATATCG
155511 AAAAAAAAA-AGAAAA
1 AAAAAAAAATAGAAAA
*
155526 AAAAAGAAAATTGAAAA
1 AAAAA-AAAATAGAAAA
*
155543 AAATAAAAAT
1 AAAAAAAAAT
155553 GTGTTTGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 5 0.22
16 9 0.39
17 9 0.39
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (16 bp):
AAAAAAAAATAGAAAA
Found at i:155542 original size:27 final size:27
Alignment explanation
Indices: 155489--155545 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
155479 TATTATTTGG
* *
155489 AAAAAGAAAAAAAAACATATCGAAAAA
1 AAAAAGAAAAAAAAAAAAATCGAAAAA
*
155516 AAAAAGAAAAAAAAAGAAAATTGAAAAA
1 AAAAAGAAAAAAAAA-AAAATCGAAAAA
155544 AA
1 AA
155546 TAAAAATGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.81, C:0.04, G:0.09, T:0.07
Consensus pattern (27 bp):
AAAAAGAAAAAAAAAAAAATCGAAAAA
Found at i:157673 original size:23 final size:23
Alignment explanation
Indices: 157647--157695 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
157637 AAACAGACAC
157647 ATTCATCCTCAACCTAAAAACGA
1 ATTCATCCTCAACCTAAAAACGA
*
157670 ATTCATCCTCAACCTAAAACCGA
1 ATTCATCCTCAACCTAAAAACGA
157693 ATT
1 ATT
157696 ATAATAGCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.31, G:0.04, T:0.24
Consensus pattern (23 bp):
ATTCATCCTCAACCTAAAAACGA
Done.